Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae

ABSTRACT Infection with carbapenem-resistant Enterobacteriaceae (CRE) has become an important challenge in health care settings and a growing concern worldwide. Since infection is preceded by colonization, an understanding of the latter may reduce CRE infections. We aimed to characterize the gut microbiota in CRE carriers, assuming that microbiota alterations precede CRE colonization. We evaluated the gut microbiota using 16S rRNA gene sequencing extracted of fecal samples collected from hospitalized CRE carriers and two control groups, hospitalized noncarriers and healthy adults. The microbiota diversity and composition in CRE-colonized patients differed from those of the control group participants. These CRE carriers displayed lower phylogenetic diversity and dysbiotic microbiota, enriched with members of the family Enterobacteriaceae. Concurrent with the enrichment in Enterobacteriaceae, a depletion of anaerobic commensals was observed. Additionally, changes in several predicted metabolic pathways were observed for the CRE carriers. Concomitantly, we found higher prevalence of bacteremia in the CRE carriers. Several clinical factors that might induce changes in the microbiota were examined and found to be insignificant between the groups. The compositional and functional changes in the microbiota of CRE-colonized patients are associated with increased risk for systemic infection. Our study results provide justification for attempts to restore the dysbiotic microbiota with probiotics or fecal transplantation. IMPORTANCE The gut microbiota plays important roles in the host’s normal function and health, including protection against colonization by pathogenic bacteria. Alterations in the gut microbial profile can potentially serve as an early diagnostic tool, as well as a therapeutic strategy against colonization by and carriage of harmful bacteria, including antibiotic-resistant pathogens. Here, we show that the microbiota of hospitalized patients demonstrated specific taxa which differed between carriers of carbapenem-resistant Enterobacteriaceae (CRE) and noncarriers. The difference in the microbiota also dictates alterations in microbiome-specific metabolic capabilities, in association with increased prevalence of systemic infection. Reintroducing specific strains and/or correction of dysbiosis with probiotics or fecal transplantation may potentially lead to colonization by bacterial taxa responsible for protection against or depletion of antibiotic-resistant pathogens.

Download Full-text

Intestinal dysbiosis in carbapenem-resistant Enterobacteriaceae carriers

10.1101/855718 ◽

2019 ◽

Cited By ~ 1

Author(s):

Hila Korach-Rechtman ◽

Maysaa Hreish ◽

Carmit Fried ◽

Shiran Gerassy-Vainberg ◽

Zaher S Azzam ◽

...

Keyword(s):

Gut Microbiota ◽

Systemic Infection ◽

16S Rrna Genes ◽

Rrna Genes ◽

Control Groups ◽

Fecal Transplantation ◽

Carbapenem Resistant ◽

Increased Risk ◽

Study Results ◽

Carbapenem Resistant Enterobacteriaceae

AbstractInfection with Carbapenem-Resistant Enterobacteriaceae (CRE) became an important challenge in health-care settings and a growing concern worldwide. Since infection is preceded by colonization, an understanding of the latter may reduce CRE-infections. We aimed to characterize the gut microbiota after colonization by CRE, assuming that an imbalanced gastrointestinal tract (GIT)-associated microbiota precedes CRE-colonization.We evaluated the GIT-microbiota using 16S rRNA genes sequencing extracted of fecal samples, collected from hospitalized CRE-carriers, and two control groups of hospitalized non-carriers and healthy adults. The microbiota diversity and composition in CRE-colonized patients differed from that of the control groups participants. These CRE-carriers displayed lower phylogenetic diversity and dysbiotic microbiota, enriched with members of the Enterobacteriaceae family. Concurrent with the bloom in Enterobacteriaceae, a depletion of anaerobic commensals was observed. Additionally, changes in several predicted metabolic pathways were observed for the CRE-carriers. Concomitant, we found higher prevalence of bacteremia in the CRE-carriers.Several clinical factors that might induce change in the microbiota were examined and found as insignificant between the groups.CRE-colonized patients have dysbiotic gut microbiota in terms of diversity and community membership, associated with increased risk for systemic infection. Our study results provides justification for attempts to restore the dysbiotic microbiota with probiotics or fecal transplantation.

Download Full-text

Microbiome Analysis Reveals the Attenuation Effect of Lactobacillus From Yaks on Diarrhea via Modulation of Gut Microbiota

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.610781 ◽

2021 ◽

Vol 10 ◽

Author(s):

Hailong Dong ◽

Bingxian Liu ◽

Aoyun Li ◽

Mudassar Iqbal ◽

Khalid Mehmood ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Pathogenic Bacteria ◽

Growth Promotion ◽

Amplicon Sequencing ◽

Treated Group ◽

Control Group ◽

Rrna Gene ◽

The Tibetan Plateau ◽

E Coli

Domestic yaks (Bos grunniens) are indigenous to the Tibetan Plateau and display a high diarrhea rate due to poor habitat and husbandry conditions. Lactobacillus has been shown to exert beneficial effects as antimicrobial, growth promotion, and gut microbiota in humans and/or murine models, but the relevant data regarding Lactobacillus isolated from yaks was unavailable. Therefore, this study aimed to investigate the effects of Lactobacillus from yaks on the intestinal microbial community in a mouse model and determine whether Lactobacillus supplementation contributed in alleviating diarrhea by modulating gut microbiota. A total of 12 ileac samples from four groups were collected for 16S rRNA gene amplicon sequencing of V3-V4 region. Results revealed that although Lactobacillus supplementation did not change the diversity of gut microbiota in mice, the proportion of some intestinal microbiota significantly changed. Specifically, the proportion of Lactobacillus and Sphingomonas in the Lactobacillus treated-group (L-group) were increased as compared to control group (C-group), whereas Pantoea, Cutibacterium, Glutamicibacter, Turicibacter, Globicatella, Microbacterium, Facklamia, unidentified_Corynebacteriaceae, Brachybacterium, and Staphylococcus were significantly decreased in the L-group. In contrast, Escherichia coli (E. coli) infection significantly decreased the proportion of beneficial bacteria such as Globicatella, Acinetobacter, Aerococcus, and Comamonas, while loads of pathogenic bacteria significantly increased including Roseburia and Megasphaera. Interestingly, Lactobacillus administration could ameliorate the microbial community structure of E. coli-induced diarrheal mice by reducing the relative abundance of pathogenic bacteria such as Paenibacillus, Aerococcus, Comamonas, Acinetobacter, Corynebacterium, Facklamia, and Globicatella. Results in this study revealed that Lactobacillus supplementation not only improved the gut microbiota but also alleviated diarrhea in mice, which may be mediated by modulating the composition and function of gut microbiota. Moreover, this study is expected to provide a new theoretical basis for the establishment of a preventive and treatment system for diarrhea in yaks.

Download Full-text

Effect of Xiaoning Liquid on Gut Microbiota in Asthmatic Mice by 16s RDNA High - Throughput Sequencing

10.21203/rs.3.rs-38586/v1 ◽

2020 ◽

Author(s):

Yuanyuan He ◽

Yating Luo ◽

Qinwan Huang ◽

Hongyun Zhou ◽

Ming Qian ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rdna ◽

High Throughput ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Control Group ◽

Rrna Gene ◽

Budesonide Group ◽

Abundance And Diversity ◽

Group Control Group

Abstract Background: To investigate the effects of Xiaoning liquid on gut microbiota in mouse during asthma.Methods: A total of 60 mice were randomly and averagely assigned to healthy control group, control group, budesonide group, and Xiaoning liquid group. The later three groups were used to establish an Ovalbumin (OVA) asthma model. The intestinal bacterial communities were compared among groups using 16S rRNA gene amplification. Analyzing the structure of gut microbiota with OTU analysis, Shannon–Wiener, PCA, PCOA, etc. 16s rDNA high- throughput sequencing. Results: The abundance and diversity of the gut microbiota in asthmatic mice increased, most obviously in the control group. The Bacteroidetes and Firmicutes levels increased in all asthmatic mice. The level of Bacteroides increased most obviously, making Bacteroides a useful marker of gut microbiota changes in asthmatic mice. The levels of Proteobacterium, Deferribacteraceae and Mucispirillum dropped significantly in the Xiaoning liquid group. Conclusions: Xiaoning liquid can reduce the species and numbers of pathogenic bacteria and restored the intestinal microecology of asthmatic mice. Xiaoning liquid has a positive effect on the function of gut microbiota.

Download Full-text

Ultrafine particles altered gut microbial population and metabolic profiles in a sex-specific manner in an obese mouse model

Scientific Reports ◽

10.1038/s41598-021-85784-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kundi Yang ◽

Mengyang Xu ◽

Jingyi Cao ◽

Qi Zhu ◽

Monica Rahman ◽

...

Keyword(s):

Ultrafine Particles ◽

Microbial Population ◽

Phosphate Buffer Solution ◽

Biodiesel Fuel ◽

Control Group ◽

Obese Mouse ◽

Rrna Gene ◽

Obese Mice ◽

Microbial Composition ◽

Increased Risk

AbstractEmerging evidence has highlighted the connection between exposure to air pollution and the increased risk of obesity, metabolic syndrome, and comorbidities. Given the recent interest in studying the effects of ultrafine particle (UFP) on the health of obese individuals, this study examined the effects of gastrointestinal UFP exposure on gut microbial composition and metabolic function using an in vivo murine model of obesity in both sexes. UFPs generated from light-duty diesel engine combustion of petrodiesel (B0) and a petrodiesel/biodiesel fuel blend (80:20 v/v, B20) were administered orally. Multi-omics approaches, including liquid chromatography–mass spectrometry (LC–MS) based targeted metabolomics and 16S rRNA gene sequence analysis, semi-quantitatively compared the effects of 10-day UFP exposures on obese C57B6 mouse gut microbial population, changes in diversity and community function compared to a phosphate buffer solution (PBS) control group. Our results show that sex-specific differences in the gut microbial population in response to UFP exposure can be observed, as UFPs appear to have a differential impact on several bacterial families in males and females. Meanwhile, the alteration of seventy-five metabolites from the gut microbial metabolome varied significantly (ANOVA p < 0.05) across the PBS control, B0, and B20 groups. Multivariate analyses revealed that the fuel-type specific disruption to the microbial metabolome was observed in both sexes, with stronger disruptive effects found in females in comparison to male obese mice. Metabolic signatures of bacterial cellular oxidative stress, such as the decreased concentration of nucleotides and lipids and increased concentrations of carbohydrate, energy, and vitamin metabolites were detected. Furthermore, blood metabolites from the obese mice were differentially affected by the fuel types used to generate the UFPs (B0 vs. B20).

Download Full-text

Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

Download Full-text

Evaluation of balance, fall risk, and related factors in patients with fibromyalgia syndrome

Turkish Journal of Physical Medicine and Rehabilitation ◽

10.5606/tftrd.2021.6273 ◽

2021 ◽

Vol 67 (4) ◽

pp. 409-415

Author(s):

Köksal Sarıhan ◽

Hülya Uzkeser ◽

Akın Erdal

Keyword(s):

Social Isolation ◽

Fall Risk ◽

Nottingham Health Profile ◽

Risk Index ◽

Control Group ◽

Healthy Individuals ◽

Increased Risk ◽

Study Results ◽

Significant Difference ◽

Risk Of Falls

Objectives: In this study, we aimed to evaluate whether fibromyalgia patients had a higher fall risk compared to healthy individuals and to identify its relationship, if there was an increase, with clinical features. Patients and methods: Between March 2018 and September 2018, a total of 50 consecutive female patients with fibromyalgia (median age: 35 years; interquantile range [IQR], 27 to 40 years) and 50 healthy female volunteers (median age: 30 years; IQR, 23 to 40 years) were included in the study. Pain was evaluated with the Visual Analog Scale (VAS), life quality with the Nottingham Health Profile (NHP), balance functions with the Berg Balance Test (BBT), and the risk of falls with a posturography device. Disease activity of fibromyalgia patients was evaluated with the Fibromyalgia Impact Questionnaire (FIQ). Results: The mean fall risk index of the fibromyalgia patients was 45%. The fall risk index was significantly higher (p=0.010) and the BBT scores were significantly lower in the patient group (p<0.001). There was a significant difference in terms of fall risk between the control group and drug-free fibromyalgia patients; however, no significant difference was found between the balance scores of the two groups. In the fibromyalgia group, a weak positive relationship was determined between the fall risk index and the social isolation subscale of the NHP. Conclusion: Our study results showed an increased risk of loss of balance and falls in fibromyalgia patients, compared to healthy individuals. This fall risk increase was also detected in fibromyalgia patients who did not use drugs. These findings suggest a possible relationship between social isolation and an increased risk of falls.

Download Full-text

A Randomised, Controlled Trial: Effect of a Multi-Strain Fermented Milk on the Gut Microbiota Recovery after Helicobacter pylori Therapy

Nutrients ◽

10.3390/nu13093171 ◽

2021 ◽

Vol 13 (9) ◽

pp. 3171

Author(s):

Eric Guillemard ◽

Marion Poirel ◽

Florent Schäfer ◽

Laurent Quinquis ◽

Caroline Rossoni ◽

...

Keyword(s):

Helicobacter Pylori ◽

Gut Microbiota ◽

Beta Diversity ◽

Pathogenic Bacteria ◽

Controlled Trial ◽

Eradication Therapy ◽

Fermented Milk ◽

Control Group ◽

Double Blind ◽

Gi Symptoms

Helicobacter pylori (Hp) eradication therapy alters gut microbiota, provoking gastrointestinal (GI) symptoms that could be improved by probiotics. The study aim was to assess the effect in Hp patients of a Test fermented milk containing yogurt and Lacticaseibacillus (L. paracasei CNCM I-1518 and I-3689, L. rhamnosus CNCM I-3690) strains on antibiotic associated diarrhea (AAD) (primary aim), GI-symptoms, gut microbiota, and metabolites. A randomised, double-blind, controlled trial was performed on 136 adults under 14-day Hp treatment, receiving the Test or Control product for 28 days. AAD and GI-symptoms were reported and feces analysed for relative and quantitative gut microbiome composition, short chain fatty acids (SCFA), and calprotectin concentrations, and viability of ingested strains. No effect of Test product was observed on AAD or GI-symptoms. Hp treatment induced a significant alteration in bacterial and fungal composition, a decrease of bacterial count and alpha-diversity, an increase of Candida and calprotectin, and a decrease of SCFA concentrations. Following Hp treatment, in the Test as compared to Control group, intra-subject beta-diversity distance from baseline was lower (padj = 0.02), some Enterobacteriaceae, including Escherichia-Shigella (padj = 0.0082) and Klebsiella (padj = 0.013), were less abundant, and concentrations of major SCFA (p = 0.035) and valerate (p = 0.045) were higher. Viable Lacticaseibacillus strains were detected during product consumption in feces. Results suggest that, in patients under Hp treatment, the consumption of a multi-strain fermented milk can induce a modest but significant faster recovery of the microbiota composition (beta-diversity) and of SCFA production and limit the increase of potentially pathogenic bacteria.

Download Full-text

Effects of Long-Term Hydrogen Intervention on Plasma Metabolites and Gut Microbiome of Rats in Health Status

10.21203/rs.3.rs-770433/v1 ◽

2021 ◽

Author(s):

Fei Xie ◽

Xue Jiang ◽

Yang Yi ◽

Zi-Jia Liu ◽

Chen Ma ◽

...

Keyword(s):

Health Status ◽

Gut Microbiota ◽

Biological Effects ◽

Enrichment Analysis ◽

The Body ◽

Plasma Metabolites ◽

Control Group ◽

Pathway Enrichment Analysis ◽

Rrna Gene

Abstract The potential for preventive and therapeutic applications of H2 have now been confirmed in various disease. However, the effects of H2 on health status have not been fully elucidated. Our previous study reported changes in the body weight and 13 serum biochemical parameters during the six-month hydrogen intervention. To obtain a more comprehensive understanding of the effects of long-term hydrogen consumption, the plasma metabolome and gut microbiota were investigated in this study. Compared with the control group, 14 and 10 differential metabolites (DMs) were identified in hydrogen-rich water (HRW) and hydrogen inhalation (HI) group, respectively. Pathway enrichment analysis showed that HRW intake mainly affected starch and sucrose metabolism, and DMs in HI group were mainly enriched in arginine biosynthesis. 16S rRNA gene sequencing showed that HRW intake induced significant changes in the structure of gut microbiota, while no marked bacterial community differences was observed in HI group. HRW intake mainly induced significant increase in the abundance of Lactobacillus, Ruminococcus, Clostridium XI, and decrease in Bacteroides. HI mainly induced decreased abundances of Blautia and Paraprevotella. The results of this study provide basic data for further research on hydrogen medicine. Determination of the effects of hydrogen intervention on microbiota profiles could also shed light on identification of mechanism underlying the biological effects of molecular hydrogen.

Download Full-text

Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-97083-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yue Hu ◽

Fang Chen ◽

Haiyong Ye ◽

Bin Lu

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rat Model ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Control Group ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Irritable Bowel

AbstractStress is one of the major causes of irritable bowel syndrome (IBS), which is well-known for perturbing the microbiome and exacerbating IBS-associated symptoms. However, changes in the gut microbiome and metabolome in response to colorectal distention (CRD), combined with restraint stress (RS) administration, remains unclear. In this study, CRD and RS stress were used to construct an IBS rat model. The 16S rRNA gene sequencing was used to characterize the microbiota in ileocecal contents. UHPLC-QTOF-MS/MS assay was used to characterize the metabolome of gut microbiota. As a result, significant gut microbial dysbiosis was observed in stress-induced IBS rats, with the obvious enrichment of three and depletion of 11 bacterial taxa in IBS rats, when compared with those in the control group (q < 0.05). Meanwhile, distinct changes in the fecal metabolic phenotype of stress-induced IBS rats were also found, including five increased and 19 decreased metabolites. Furthermore, phenylalanine, tyrosine and tryptophan biosynthesis were the main metabolic pathways induced by IBS stress. Moreover, the altered gut microbiota had a strong correlation with the changes in metabolism of stress-induced IBS rats. Prevotella bacteria are correlated with the metabolism of 1-Naphthol and Arg.Thr. In conclusion, the gut microbiome, metabolome and their interaction were altered. This may be critical for the development of stress-induced IBS.

Download Full-text

The Effects of Chinese Medicine QRD, Antibiotics, and Probiotics on Therapy and Gut Microbiota in Septic Rats

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.712028 ◽

2021 ◽

Vol 11 ◽

Author(s):

Huiling Cao ◽

Chunhui Zong ◽

Wenkui Dai ◽

Qiaoying Gao ◽

Donghua Li ◽

...

Keyword(s):

Chinese Medicine ◽

Gut Microbiota ◽

Survival Rates ◽

Amplicon Sequencing ◽

Medical Emergency ◽

Control Group ◽

Rrna Gene ◽

Sham Operation ◽

Therapeutic Effects

Sepsis is a common and often treacherous medical emergency with a high mortality and long-term complications in survivors. Though antibiotic therapy can reduce death rate of sepsis significantly, it impairs gut microbiota (GM), which play imperative roles in human health. In this study, we compared the therapeutic effects of antibiotics, probiotics, and Chinese medicine QRD on the survival rates of septic model and observed the GM characteristics of experimental rats via 16S rRNA gene amplicon sequencing. The 72 h survival rates of septic rat demonstrated the significant therapeutic effects in the three groups treated with antibiotics (AT), Chinses medicine QRD (QT), and probiotics (PT), which were elevated from the survival rate of 26.67% for the sepsis control group (ST) to 100.0% for AT, 88.24% for QT, and 58.33% for PT. The original characteristics of GM identified in the sham operation controls (SC) were relatively similar to those in PT and QT; nevertheless, the AT rats were shown dramatically decreased in the GM diversity. In addition, the septic rats in AT were revealed the higher abundances of Escherichia Shigella, Proteus, Morganella, Enterococcus, and Lysinibacillus, but the lower those of Parabacteroides, Alistipes, Desulfovibrio, Bacteroides, Helicobacter, Mucispirillum, Oscillibacter, Lachnospiraceae, and Ruminiclostridium 9, when compared to the PT and QT rats. By contrast, the GM of PT and QT rats shared similar diversity and structure. Our findings indicated that QRD increased the survival rates without impairment of the GM characteristics, which provides novel insights into the role of Chinese medicine in therapy and long-term recovery of sepsis.

Download Full-text