scholarly journals The Gut Microbiome and Resistome of Healthy Volunteers are Restructured After Short Courses of Antibiotics

2020 ◽  
Vol 41 (S1) ◽  
pp. s5-s6
Author(s):  
Winston Anthony ◽  
Kimberley Sukhum ◽  
Candice Cass ◽  
Kimberly Reske ◽  
Sondra Seiler ◽  
...  
Keyword(s):  
Healthy Volunteers ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Community Diversity ◽  
Metabolic Profiles ◽  
Innate Resistance ◽  
Starting Point ◽  
Stool Samples ◽  
Stool Specimens ◽  
Short Courses

Background: Antimicrobial exposure is a significant risk factor for the development of antibiotic-resistant organisms (ARO); however, the depth and duration of this impact is not well described. The study goal is to define impact of antibiotics on the gut microbiome of healthy volunteers (HVs). Methods: HVs were randomized to receive either 5 days of levofloxacin (LVX), azithromycin (AZM), cefpodoxime (CPD), or AZM + CPD (Fig. 1). Stool samples were collected at 15 time points per patient before, during, and after antibiotics. Remnant stool samples from the microbiology laboratory were collected from patients admitted to the medical intensive care unit (MICU) as a comparison of the microbiome in a critically ill state. DNA was extracted from samples and was submitted for shotgun sequencing. Relative abundance, resistome, and metabolic pathway abundance of bacterial taxa were determined and statistical analysis conducted in R software. Results: In total, 289 stool specimens from 20 HVs, and 26 remnant stool specimens were obtained from patients admitted from the MICU (Fig. 1). Community diversity and richness decreased in the first week post-ABX for all HVs (P < .01). Linear discriminant analysis identified Bacteroides and Clostridium as taxonomic groups enriched after CPD, while AZM and LVX produced a relative abundance increase in diverse Firmicutes spp. Longitudinal tracking confirmed that after all antibiotics except LVX, HV microbiomes lost species diversity and shifted toward a state similar to that observed in MICU patients (Fig. 2). The gut microbiome of most HVs exhibited resiliency and returned to a higher diversity level similar to their starting point; however, 10% of HVs did not. Moreover, antibiotic-specific increases in resistance markers reveal innate resistance to β-lactams and macrolides within the gut microbiome of the HVs. Finally, HV microbiomes, which shifted toward a MICU-like taxonomic state, also clustered with microbial metabolic profiles from MICU patients.The HV microbial metabolic profiles were significantly enriched for important biosynthesis pathways producing chorismate and polysaccharides. MICU patient gut microbiomes were enriched for fatty acid regulation and quinolone biosynthesis, and for many degradation pathways important for different aspects of antibiotic resistance such as membrane integrity, alternative respiration, and antibiotic inactivation. Conclusions: Short courses of antibiotics can cause acute and chronic microbiome disruptions in HVs, as evidenced by decreased microbiome diversity and increases in specific innate resistance elements. These data support the need for antimicrobial stewardship to support rationale antibiotic use to prevent gut microbiome disruptions.Funding: CDC BAA 200-2016-91962Disclosures: None

Effect of prophylactic dextrose gel on the neonatal gut microbiome

2021 ◽  
pp. fetalneonatal-2021-322757
Author(s):  
Sophie L St Clair ◽  
Jane E Harding ◽  
Justin M O’Sullivan ◽  
Gregory D Gamble ◽  
Jane M Alsweiler ◽  
...  
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Community Stability ◽  
Neonatal Hypoglycaemia ◽  
Bacterial Dna ◽  
Dna Concentration ◽  
Stool Samples

ObjectiveTo determine the effect of prophylactic dextrose gel on the infant gut microbiome.DesignObservational cohort study nested in a randomised trial.SettingThree maternity hospitals in New Zealand.PatientsInfants at risk of neonatal hypoglycaemia whose parents consented to participation in the hypoglycaemia Prevention in newborns with Oral Dextrose trial (hPOD). Infants were randomised to receive prophylactic dextrose gel or placebo gel, or were not randomised and received no gel (controls). Stool samples were collected on days 1, 7 and 28.Main outcome measuresThe primary outcome was microbiome beta-diversity at 4 weeks. Secondary outcomes were beta-diversity, alpha-diversity, bacterial DNA concentration, microbial community stability and relative abundance of individual bacterial taxa at each time point.ResultsWe analysed 434 stool samples from 165 infants using 16S rRNA gene amplicon sequencing. There were no differences between groups in beta-diversity at 4 weeks (p=0.49). There were also no differences between groups in any other microbiome measures including beta-diversity (p=0.53 at day 7), alpha-diversity (p=0.46 for day 7 and week 4), bacterial DNA concentration (p=0.91), microbial community stability (p=0.52) and microbial relative abundance at genus level. There was no evidence that exposure to any dextrose gel (prophylaxis or treatment) had any effect on the microbiome. Mode of birth, type of milk fed, hospital of birth and ethnicity were all associated with differences in the neonatal microbiome.ConclusionsClinicians and consumers can be reassured that dextrose gel used for prophylaxis or treatment of neonatal hypoglycaemia does not alter the neonatal gut microbiome.Trial registration number12614001263684.

scholarly journals Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12033
Author(s):  
Yi-ran Chen ◽  
Qin-long Jing ◽  
Fang-lan Chen ◽  
Huimin Zheng ◽  
Li-dan Chen ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Large Scale ◽  
Community Diversity ◽  
Human Populations ◽  
Human Intestine ◽  
Adverse Health Effects ◽  
Waist Size ◽  
Host Health ◽  
The Relationship

Desulfovibrio (DSV) is frequently found in the human intestine but limited knowledge is available regarding the relationship between DSV and host health. In this study, we analyzed large-scale cohort data from the Guangdong Gut Microbiome Project to study the ecology of DSV and the associations of DSV and host health parameters. Phylogenetic analysis showed that Desulfovibrio piger might be the most common and abundant DSV species in the GGMP. Predominant sub-OTUs of DSV were positively associated with bacterial community diversity. The relative abundance of DSV was positively correlated with beneficial genera, including Oscillospira, Coprococcus,Ruminococcus,Akkermansia, Roseburia,Faecalibacterium, andBacteroides, and was negatively associated with harmful genera, such as Clostridium,Escherichia,Klebsiella, and Ralstonia. Moreover, the relative abundance of DSV was negatively correlated with body mass index, waist size, triglyceride levels, and uric acid levels. This suggests that DSV is associated with healthy hosts in some human populations.

scholarly journals Gut microbiome in cirrhotic hepatitis C virus patients with and without hepatocellular carcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Khaled Mohieldeen ◽  
Soraya Abdel Fatah Hamoda ◽  
Shwikar Mahmoud Ahmed ◽  
Abdurrahman Najeeb ◽  
Walid Ismail Ellakany
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis C ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Control Group ◽  
Microbial Dysbiosis ◽  
Egyptian Patients ◽  
Stool Specimens ◽  
Abundance And Diversity ◽  
And Control

Abstract Background Chronic hepatitis C is the most common cause of chronic liver disease and hepatocellular carcinoma in Egypt. A pathogenic link with gut microbial dysbiosis has been described in different diseases. The aim of the study is to elucidate changes in gut microbiome in cirrhotic HCV Egyptian patients with and without HCC. Results The study included 50 cirrhotic HCV patients; 25 with and 25 without HCC and 25 healthy controls with matched age and sex. Stool specimens were taken from all participants. Quantitative SYBR Green real-time PCR technique targeting 16S rRNA was done for the identification and quantitation of selected bacterial phylum, genera, and/or species. Both HCC and cirrhosis groups showed decrease in Firmicutes, F/B ratio, A. mucinophilia, and F. prausnitzii compared to the control group. However, the HCC group only showed statistically significant increase in Bacteroides and Lactobacilli, and decrease of Prevotella relative abundance and P/B ratio compared to both cirrhosis and control groups. As regard the relation between the gut microbiome and stages of HCC, BCLC stage D showed significantly the lowest relative abundance of Ruminococcus. Conclusion Patients with HCV-related cirrhosis and HCC exhibit microbial dysbiosis; altered microbial relative abundance and diversity with HCC patients showing higher proinflammatory bacteria compared to cirrhotics.

scholarly journals The Adult Phenylketonuria (PKU) Gut Microbiome

2021 ◽  
Vol 9 (3) ◽  
pp. 530
Author(s):  
Viviana J. Mancilla ◽  
Allison E. Mann ◽  
Yan Zhang ◽  
Michael S. Allen
Keyword(s):  
Gut Microbiome ◽  
Community Diversity ◽  
Rrna Gene ◽  
Dietary Interventions ◽  
Dietary Restrictions ◽  
Stool Samples ◽  
Phenylalanine Metabolism ◽  
Restrictive Diet ◽  
And Control ◽  
Amino Acid Formula

Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 region of the 16S rRNA gene from stool samples collected from adults with PKU (n = 11) and non-PKU controls (n = 21). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria. Gut community diversity was lower in PKU individuals, though this effect was only statistically suggestive. A total of 65 genera across 5 phyla were statistically differentially abundant between PKU and control samples (p < 0.001). Additionally, we identified six metabolic pathways that differed between groups (p < 0.05), with four enriched in PKU samples and two in controls. While the child PKU gut microbiome has been previously investigated, this is the first study to explore the gut microbiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKU adults and highlights the need for further studies to understand the effects of dietary restrictions.

scholarly journals Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery

Life ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 246
Author(s):  
Felix C.F. Schmitt ◽  
Martin Schneider ◽  
William Mathejczyk ◽  
Markus A. Weigand ◽  
Jane C. Figueiredo ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Postoperative Complications ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Tumor Resection ◽  
Microbial Composition ◽  
Colorectal Cancer Surgery ◽  
Long Term Changes ◽  
Stool Samples

Changes in the gut microbiome have already been associated with postoperative complications in major abdominal surgery. However, it is still unclear whether these changes are transient or a long-lasting effect. Therefore, the aim of this prospective clinical pilot study was to examine long-term changes in the gut microbiota and to correlate these changes with the clinical course of the patient. Methods: In total, stool samples of 62 newly diagnosed colorectal cancer patients undergoing primary tumor resection were analyzed by 16S-rDNA next-generation sequencing. Stool samples were collected preoperatively in order to determine the gut microbiome at baseline as well as at 6, 12, and 24 months thereafter to observe longitudinal changes. Postoperatively, the study patients were separated into two groups—patients who suffered from postoperative complications (n = 30) and those without complication (n = 32). Patients with postoperative complications showed a significantly stronger reduction in the alpha diversity starting 6 months after operation, which does not resolve, even after 24 months. The structure of the microbiome was also significantly altered from baseline at six-month follow-up in patients with complications (p = 0.006). This was associated with a long-lasting decrease of a large number of species in the gut microbiota indicating an impact in the commensal microbiota and a long-lasting increase of Fusobacterium ulcerans. The microbial composition of the gut microbiome shows significant changes in patients with postoperative complications up to 24 months after surgery.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Parasitic infections in Swiss children: Are we overtesting?

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Corinne Légeret ◽  
Céline Rüttimann ◽  
Hans Fankhauser ◽  
Henrik Köhler
Keyword(s):  
Retrospective Study ◽  
Positive Result ◽  
Pediatric Patients ◽  
Intestinal Parasites ◽  
Gastrointestinal Symptoms ◽  
International Travel ◽  
Parasitic Infections ◽  
Stool Samples ◽  
Stool Specimens

Abstract Background A wide variation of causes can lead to gastrointestinal symptoms in children- an infection with parasites is one of them. The expansion of international travel might lead to an increase in testing children for a correspondent infection. Currently there are no guidelines available, which patients should be tested for a possible parasitical infection. The aim of the study was to characterize Swiss children suffering from intestinal parasites, in order to provide more knowledge for the clinician who should be tested. Methods This is a retrospective study of Swiss pediatric patients, whose stools have been tested for parasites and helminths. Results A total of 1855 stool samples, belonging to 572 different children with an average age of 7.9 years, were tested within a 10-year period. The prevalence of a positive result was 4.2%, of which all were positive for Blastocystis, and 12.5% had a co-infection with Endolimax nana. Conclusion Immigrants, immune compromised children with diarrhea and pediatric patients with bloody or protracted diarrhea should have 2 different stool specimens examined for a possible parasitical infection.

scholarly journals A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Christophe Lay ◽  
Collins Wenhan Chu ◽  
Rikky Wenang Purbojati ◽  
Enzo Acerbi ◽  
Daniela I. Drautz-Moses ◽  
...  
Keyword(s):  
Risk Factor ◽  
Gut Microbiome ◽  
Reference Group ◽  
Mode Of Delivery ◽  
Controlled Study ◽  
Double Blind ◽  
Lipopolysaccharide Biosynthesis ◽  
Infant Gut Microbiome ◽  
Stool Samples ◽  
The Impact

Abstract Background The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. Results As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. Conclusions This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. Trial registration The study was registered in the Dutch Trial Register (Number: 2838) on 4th April 2011.

scholarly journals Gut Microbiome Composition Remains Stable in Individuals with Diabetes-Related Early to Late Stage Chronic Kidney Disease

Biomedicines ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
Ashani Lecamwasam ◽  
Tiffanie M. Nelson ◽  
Leni Rivera ◽  
Elif I. Ekinci ◽  
Richard Saffery ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Relative Abundance ◽  
Cross Sectional Study ◽  
Early Event ◽  
Sectional Study ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Late Stages

(1) Background: Individuals with diabetes and chronic kidney disease display gut dysbiosis when compared to healthy controls. However, it is unknown whether there is a change in dysbiosis across the stages of diabetic chronic kidney disease. We investigated a cross-sectional study of patients with early and late diabetes associated chronic kidney disease to identify possible microbial differences between these two groups and across each of the stages of diabetic chronic kidney disease. (2) Methods: This cross-sectional study recruited 95 adults. DNA extracted from collected stool samples were used for 16S rRNA sequencing to identify the bacterial community in the gut. (3) Results: The phylum Firmicutes was the most abundant and its mean relative abundance was similar in the early and late chronic kidney disease group, 45.99 ± 0.58% and 49.39 ± 0.55%, respectively. The mean relative abundance for family Bacteroidaceae, was also similar in the early and late group, 29.15 ± 2.02% and 29.16 ± 1.70%, respectively. The lower abundance of Prevotellaceae remained similar across both the early 3.87 ± 1.66% and late 3.36 ± 0.98% diabetic chronic kidney disease groups. (4) Conclusions: The data arising from our cohort of individuals with diabetes associated chronic kidney disease show a predominance of phyla Firmicutes and Bacteroidetes. The families Ruminococcaceae and Bacteroidaceae represent the highest abundance, while the beneficial Prevotellaceae family were reduced in abundance. The most interesting observation is that the relative abundance of these gut microbes does not change across the early and late stages of diabetic chronic kidney disease, suggesting that this is an early event in the development of diabetes associated chronic kidney disease. We hypothesise that the dysbiotic microbiome acquired during the early stages of diabetic chronic kidney disease remains relatively stable and is only one of many risk factors that influence progressive kidney dysfunction.

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