Proteus mirabilis Utilizes a Contact Dependent Growth Inhibition System to Kill Competitor Species

The microbial organisms that colonize the human body are more abundant than somatic cells and contain more genes than the human genome. An estimated 500–1000 species of bacteria exist in and on the human body. The composition of polymicrobial communities in locations such as the gut and the urinary tract is shaped by the host but also by cooperative and competitive interactions between species. The study of bacterial competition systems has received significant attention in recent years, as they represent promising narrow-spectrum tools to eliminate pathogenic species. However, only few interbacterial competition systems have been identified and many more remain to be discovered. We observed competition between two common gut commensal bacteria that could be due to the action of a new competition system. In the gut of neonatal mice, commensal Proteus mirabilis eliminated Escherichia coli. We replicated this phenotype in vitro and demonstrated that mouse P. mirabilis killed Gram negative bacteria. However, P. mirabilis could not kill Gram positive or eukaryotic target cells. Killing required direct contact between P. mirabilis and its target cells, but killing was independent of the Type 6 Secretion System (T6SS), which is the only contact-dependent killing system described for P. mirabilis. The killing system was regulated by components secreted into the supernatant. Target cells lost nucleoid integrity and reduced transcription and metabolic activity. Through genomic comparison, we discovered that P. mirabilis encodes for a Contact Dependent growth Inhibition (CDI) system. The CDI system is a two-partner secretion system wherein the CdiB protein exports and displays its partner CdiA, the effector toxic protein. CDI producer cells are protected by an immunity protein, CdiI. A P. mirabilis mutant in the cdiA toxin did not kill target cells. Additionally, heterologous expression of the immunity gene rescued viability of E. coli in co-culture with P. mirabilis. Based on sequence homology, we grouped Proteus CDI systems into three classes. To our knowledge, this is the first report of CDI-mediated interbacterial competition for P. mirabilis. This system could be used by P. mirabilis to eliminate competitor species during a polymicrobial infection

The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster.

BackgroundThe root extract of Rhodiola rosea has historically been used in Europe and Asia as an adaptogen, and similar to ginseng and Shisandra, shown to display numerous health benefits in humans, such as decreasing fatigue and anxiety while improving mood, memory, and stamina. A similar extract in the Rhodiola family, Rhodiola crenulata, has previously been shown to confer positive effects on the gut homeostasis of the fruit fly, Drosophila melanogaster. Although, R. rosea has been shown to extend lifespan of many organisms such as fruit flies, worms and yeast, its anti-aging mechanism remains uncertain. Using D. melanogaster as our model system, the purpose of this work was to examine whether the anti-aging properties of R. rosea are due to its impact on the microbial composition of the fly gut.ResultsRhodiola rosea treatment significantly increased the abundance of Acetobacter, while subsequently decreasing the abundance of Lactobacillales of the fly gut at 10 and 40 days of age. Additionally, supplementation of the extract decreased the total culturable bacterial load of the fly gut, while increasing the overall quantifiable bacterial load. The extract did not display any antimicrobial activity when disk diffusion tests were performed on bacteria belonging to Microbacterium, Bacillus, and Lactococcus.ConclusionsUnder standard and conventional rearing conditions, supplementation of R. rosea significantly alters the microbial community of the fly gut, but without any general antibacterial activity. Further studies should investigate whether R. rosea impacts the gut immunity across multiple animal models and ages

The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

Abstract Background The root extract of Rhodiola rosea has historically been used in Europe and Asia as an adaptogen, and similar to ginseng and Shisandra, shown to display numerous health benefits in humans, such as decreasing fatigue and anxiety while improving mood, memory, and stamina. A similar extract in the Rhodiola family, Rhodiola crenulata, has previously been shown to confer positive effects on the gut homeostasis of the fruit fly, Drosophila melanogaster. Although, R. rosea has been shown to extend lifespan of many organisms such as fruit flies, worms and yeast, its anti-aging mechanism remains uncertain. Using D. melanogaster as our model system, the purpose of this work was to examine whether the anti-aging properties of R. rosea are due to its impact on the microbial composition of the fly gut. Results Rhodiola rosea treatment significantly increased the abundance of Acetobacter, while subsequently decreasing the abundance of Lactobacillales of the fly gut at 10 and 40 days of age. Additionally, supplementation of the extract decreased the total culturable bacterial load of the fly gut, while increasing the overall quantifiable bacterial load. The extract did not display any antimicrobial activity when disk diffusion tests were performed on bacteria belonging to Microbacterium, Bacillus, and Lactococcus. Conclusions Under standard and conventional rearing conditions, supplementation of R. rosea significantly alters the microbial community of the fly gut, but without any general antibacterial activity. Further studies should investigate whether R. rosea impacts the gut immunity across multiple animal models and ages

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Additional file 2: Table S1. OTU table provided by 16S rRNA amplicon sequencing of female D. melanogaster at early and late stages of the fly lifespan

MOESM1 of The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

Additional file 1: Figure S1. qRT-PCR and CFU analysis of male D. melanogaster at early and late stages of the fly lifespan

The impact of Rhodiola rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model.

Type 2 diabetes is the most prevalent endocrine disease in the world, and recently the gut microbiota have become a potential target for its management. Recent studies have illustrated that this disease may predispose individuals to certain microbiome compositions, and treatments like metformin have been shown to change gut microbiota and their associated metabolic pathways. However, given the limitations and side effects associated with pharmaceuticals currently being used for therapy of diabetes, there is a significant need for alternative treatments. In this study, we investigated the effects of a root extract from Rhodiola rosea in a Leptin receptor knockout (db/db) mouse model of type 2 diabetes. Our previous work showed that Rhodiola rosea had anti-inflammatory and gut microbiome-modulating properties, while extending lifespan in several animal models. In this study, treatment with Rhodiola rosea improved fasting blood glucose levels, altered the response to exogenous insulin, and decreased circulating lipopolysaccharide and hepatic C-reactive protein transcript levels. We hypothesize that these changes may in part reflect the modulation of the microbiota, resulting in improved gut barrier integrity and decreasing the translocation of inflammatory biomolecules into the bloodstream. These findings indicate that Rhodiola rosea is an attractive candidate for further research in the management of type 2 diabetes

Assessing the prevalence and treatment of malnutrition in hospitalized children in Mofid Children's Hospital during 2015-2016

Background: Malnutrition in hospitalized patients causes problems in treatment and increases hospitalization duration. The aim of this research was to determine the prevalence of malnutrition in hospitalized children. Methods: Children aged 1 month to 18 years (n = 1186) who were admitted to medical and surgery wards of Mofid children’s hospital from November 2015 to February 2016, entered the study. We measured different anthropometric variables in patients with malnutrition. Also, nutritional counseling was performed and three months follow-up was done. Results: Patient data were registered in questionnaires particularly for children 2 years old and less. 597 children under 2 years of age and 607 children over two years entered the study. The data analysis was done by SPSS version 22.0 (Chicago, IL, USA). The t test inferential method was used in comparing variables. P values less than 0.05 were considered statistically significant. Based on the body mass index (BMI) Z score, and in accordance with the World Health Organization (WHO) cut-off, among children over 2 years, 9% were diagnosed as overweight or obese, 54% were within the normal range and 37% were underweight at time of admission. In the underweight group, 43% were mildly, 21.2% were moderately and 35.8% were severely underweight. Based on the weight for length Z score in patients less than 2 years of age at time of admission, 6% were overweight, 60% were in normal range and 34% were underweight. Among children with malnutrition, 21% had mild, 3.0% had moderate and 10% had severe malnutrition. No significant meaningful relation was found between prevalence of malnutrition and severity of illness. In the moderate to severe undernutrition group, nutritionist counseling was done. Comparison of BMI and weight, before and after admission (the baseline and the follow up visits), was done by means of repeated measurements. Comparison of the patient’s weight at time of admission with weight at 1, 2 and 3 months after the first nutritional consultation showed statistically meaningful difference (P value < 0.05). Conclusion: Growth indices need to be evaluated in every hospitalized child. Nutritional consultation is useful in children with malnutrition. The main purpose of early diagnosis of malnutrition is to prevent its progression, and also to design a useful, applicable and cost-effective nutritional intervention for malnutrition treatment

Assessing the prevalence and treatment of malnutrition in hospitalized children in Mofid Children's Hospital during 2015-2016

Background: Malnutrition in hospitalized patients causes problems in treatment and increases hospitalization duration. The aim of this research was to determine the prevalence of malnutrition in hospitalized children. Methods: Children aged 1 month to 18 years (n = 1186) who were admitted to medical and surgery wards of Mofid children’s hospital from November 2015 to February 2016, entered the study. We measured different anthropometric variables in patients with malnutrition. Also, nutritional counseling was performed and three months follow-up was done. Results: Patient data were registered in questionnaires particularly for children 2 years old and less. 597 children under 2 years of age and 607 children over two years entered the study. The data analysis was done by SPSS version 22.0 (Chicago, IL, USA). The t test inferential method was used in comparing variables. P values less than 0.05 were considered statistically significant. Based on the body mass index (BMI) Z score, and in accordance with the World Health Organization (WHO) cut-off, among children over 2 years, 9% were diagnosed as overweight or obese, 54% were within the normal range and 37% were underweight at time of admission. In the underweight group, 43% were mildly, 21.2% were moderately and 35.8% were severely underweight. Based on the weight for length Z score in patients less than 2 years of age at time of admission, 6% were overweight, 60% were in normal range and 34% were underweight. Among children with malnutrition, 21% had mild, 3.0% had moderate and 10% had severe malnutrition. No significant meaningful relation was found between prevalence of malnutrition and severity of illness. In the moderate to severe undernutrition group, nutritionist counseling was done. Comparison of BMI and weight, before and after admission (the baseline and the follow up visits), was done by means of repeated measurements. Comparison of the patient’s weight at time of admission with weight at 1, 2 and 3 months after the first nutritional consultation showed statistically meaningful difference (P value < 0.05). Conclusion: Growth indices need to be evaluated in every hospitalized child. Nutritional consultation is useful in children with malnutrition. The main purpose of early diagnosis of malnutrition is to prevent its progression, and also to design a useful, applicable and cost-effective nutritional intervention for malnutrition treatment

ai-corona: Radiologist-assistant deep learning framework for COVID-19 diagnosis in chest CT scans.

The development of medical assisting tools based on artificial intelligence advances is essential in the global fight against COVID-19 outbreak and the future of medical systems. In this study, we introduce ai-corona, a radiologist-assistant deep learning framework for COVID-19 infection diagnosis using chest CT scans. Our framework incorporates an EfficientNetB3-based feature extractor. We employed three datasets; the CC-CCII set, the MasihDaneshvari Hospital (MDH) cohort, and the MosMedData cohort. Overall, these datasets constitute 7184 scans from 5693 subjects and include the COVID-19, non-COVID abnormal (NCA), common pneumonia (CP), non-pneumonia, and Normal classes. We evaluate ai-corona on test sets from the CC-CCII set, MDH cohort, and the entirety of the MosMedData cohort, for which it gained AUC scores of 0.997, 0.989, and 0.954, respectively. Our results indicates ai-corona outperforms all the alternative models. Lastly, our framework's diagnosis capabilities were evaluated as assistant to several experts. Accordingly, We observed an increase in both speed and accuracy of expert diagnosis when incorporating ai-corona's assistance