scholarly journals Integrated Metagenomic and Transcriptomic Analyses Reveal the Dietary Dependent Recovery of Host Metabolism From Antibiotic Exposure

2021 ◽  
Vol 9 ◽  
Author(s):  
Bingbing Li ◽  
Huihui Qiu ◽  
Ningning Zheng ◽  
Gaosong Wu ◽  
Yu Gu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Differentially Expressed Gene ◽  
Endocrine System ◽  
Chow Diet ◽  
Metagenomic Sequencing ◽  
Antibiotic Exposure ◽  
Short Term ◽  
Functional Changes ◽  
Host Metabolism

The balance of gut microbiome is essential for maintaining host metabolism homeostasis. Despite widespread antibiotic use, the potential long-term detrimental consequences of antibiotics for host health are getting more and more attention. However, it remains unclear whether diet affects the post-antibiotic recovery of gut microbiome and host metabolism. In this study, through metagenomic sequencing and hepatic transcriptome analysis, we investigated the divergent impacts of short-term vancomycin (Vac), or combination of ciprofloxacin and metronidazole (CM) treatment on gut microbiome and host metabolism, as well as their recovery extent from antibiotic exposure on chow diet (CD) and high-fat diet (HFD). Our results showed that short-term Vac intervention affected insulin signaling, while CM induced more functional changes in the microbiome. However, Vac-induced long-term (45 days) changes of species were more apparent when recovered on CD than HFD. The effects of antibiotic intervention on host metabolism were long-lasting, antibiotic-specific, and diet-dependent. The number of differentially expressed gene was doubled by Vac than CM, but was comparable after recovery on CD as revealed by the hepatic transcriptomic analysis. In contrast, HFD intake during recovery could worsen the extent of post-antibiotic recovery by altering infection, immunity, and cancer-related pathways in short-term Vac-exposed rats and by shifting endocrine system-associated pathways in CM-exposed rats. Together, the presented data demonstrated the long-term recovery extent after different antibiotic exposure was diet-related, highlighting the importance of dietary management during post-antibiotic recovery.

scholarly journals Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Travis T. Sims ◽  
Molly B. El Alam ◽  
Tatiana V. Karpinets ◽  
Stephanie Dorta-Estremera ◽  
Venkatesh L. Hegde ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Radiation Therapy ◽  
Gut Microbiota ◽  
Cancer Patients ◽  
Gut Microbiome ◽  
Compositional Variation ◽  
Short Term ◽  
Microbiome Diversity ◽  
Term Survivor

AbstractDiversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. Modulation of the gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.

scholarly journals Long-term exposure to TET increases body weight of juvenile zebrafish as indicated in host metabolism and gut microbiome

2020 ◽  
Vol 139 ◽  
pp. 105705 ◽  
Author(s):  
Tharushi Prabha Keerthisinghe ◽  
Feng Wang ◽  
Mengjing Wang ◽  
Qin Yang ◽  
Jiawei Li ◽  
...  
Keyword(s):  
Body Weight ◽  
Gut Microbiome ◽  
Host Metabolism

scholarly journals Weaning age and its effect on the development of the swine gut microbiome and resistome

2021 ◽  
Author(s):  
Devin B Holman ◽  
Katherine E Gzyl ◽  
Kathy T Mou ◽  
Heather K Allen
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Carbohydrate Active Enzymes ◽  
Fecal Microbiome ◽  
Shotgun Metagenomic Sequencing ◽  
Swine Operations ◽  
Weaning Age

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. In this study, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 21 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that pigs tend to have a more similar microbiome as they age and that weaning age has only a temporary effect on the gut microbiome.

scholarly journals The Time-Dependent Dynamics of Gut Microbiota and the Interaction With Host Metabolism in Mouse Pulmonary Fibrosis Models

2021 ◽  
Author(s):  
Xiao-Hui Yang ◽  
Xiu-Juan Jia ◽  
Xiao-Sa Chi ◽  
Xiao-Meng Wang ◽  
Fang-Fang Wang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Pulmonary Fibrosis ◽  
Gut Microbiome ◽  
Metabolic Changes ◽  
Time Dependent ◽  
Punicic Acid ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
Serum Metabolites ◽  
Host Metabolism

Abstract Background: Pulmonary fibrosis (PF) is a chronic progressive disease whose pathogenesis is thought to be associated with activation of the immune system and consequent metabolic changes. Recent studies suggested that gut microbes are closely related with host's immune response and metabolic changes in fibrotic hosts. However, the dynamic changes of the gut microbiome and the interaction profiles with host metabolism during the development of pulmonary fibrosis remain inconclusive. Results: We collected serum and fecal samples from bleomycin-induced fibrotic mice at 0, 7, 14, and 28 days and performed UPLC-MS analysis on serum metabolites and metagenomic sequencing on fecal samples. It is found that the serum metabolic profile and gut microbiome were significantly altered in mice during the progression of fibrosis. Among the serum metabolites, the levels of three major types of lipids, i.e., glycerolipids, glycerophospholipids, and fatty acids exhibit significant time-dependent changes. The glycerolipid TG and multiple glycerophospholipids (3 PG, 6 PE, and 1 PC) decreased in the early stage of fibrosis and increased in the late stage. The other two types of glycerolipids MG and DG and the fatty acids Cartinine and Punicic acid decreased through the development of fibrosis. In the meantime, we detected significantly elevated abundance of gut microbiome taxa, including Prevotella sp. from Bacteroidetes, Lactobacillus from Firmicutes, and Bifidobacterium from Actinobacteria in mice with pulmonary fibrosis. When compared to the dynamic profiles of serum metabolites, the abundances of gut microbiome show a high level of correlation with that of serum metabolites. The taxa from Bacteroides, such as Butyricimonas_synergistica and Muribaculaceae, show positive correlation with the cluster of glycerophospholipids, while taxa from Firmicutes, such as Clostridioides difficile and Enterococcus faecium exhibit negative correlation. Further functional classification suggested that those taxa are involved in multiple functional modules, such as Transporters, Secretion system, and Metabolism. Conclusions: The results reveal the synergistic changes between the gut microbiome and host metabolism and the dynamic responses of gut microbiome to host fibrosis during the progression of fibrosis.

Short-term Resistance Training Increases APPL1 Content in the Liver and the Insulin Sensitivity of Mice Fed a Long-term High-fat Diet

2019 ◽  
Vol 128 (01) ◽  
pp. 30-37
Author(s):  
Luciele Guerra Minuzzi ◽  
Gabriel Keine Kuga ◽  
Leonardo Breda ◽  
Rafael Calais Gaspar ◽  
Vitor Rosetto Muñoz ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
Resistance Training ◽  
High Fat Diet ◽  
Calorie Intake ◽  
Hepatic Tissue ◽  
Chow Diet ◽  
Adapter Protein ◽  
High Fat ◽  
Short Term

Abstract Background APPL1, an adapter protein, interact directly with adiponectin receptors mediating adiponectin signaling and acting as a critical regulator of the crosstalk between adiponectin and insulin signaling pathway. The inadequate level of physical activity, high-calorie intake, or both lead to adverse consequences on health, like insulin resistance. On the order hand, physical exercise acts positively in the insulin action. Purpose Here, we investigated the effects of short-term resistance training (RT) on APPL1 content and adiponectin pathway in the liver of mice fed a long-term high-fat diet. Methods Swiss mice were distributed into 3 groups: Mice that fed a chow diet (CTR); Mice fed a high-fat diet for 16 months (HFD); and mice fed a high-fat diet for 16 months and submitted to a climbing ladder exercise (RT) for 7 days (HFD-EXE). Results The results show that short-term RT increases the APPL1 content but wasn’t able to alter AdipoR1 and AdipoR2 content in the liver of HFD-EXE mice. However, this increase in the APPL1 content in response to RT was accompanied by improvement in the insulin sensitivity. Conclusion In summary, our data suggested that short-term RT improves glycemic homeostasis and increases APPL1 in the hepatic tissue of mice treated with long-term high-fat diet.

scholarly journals Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly

2019 ◽  
Vol 20 (S16) ◽  
Author(s):  
Joyce B. Kang ◽  
Benjamin A. Siranosian ◽  
Eli L. Moss ◽  
Niaz Banaei ◽  
Tessa M. Andermann ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Gut Microbiome ◽  
Draft Genome ◽  
Strain Level ◽  
Comparative Genomic ◽  
Metagenomic Sequencing ◽  
Antibiotic Exposure ◽  
E Coli ◽  
Selective Pressures ◽  
Antimicrobial Resistance Genes

Abstract Background Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure. Results Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject’s gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject’s E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli. Conclusion This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.

scholarly journals Antibiotic Exposure Has Sex-Dependent Effects on the Gut Microbiota and Metabolism of Short-Chain Fatty Acids and Amino Acids in Mice

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Hongchang Gao ◽  
Qi Shu ◽  
Jiuxia Chen ◽  
Kai Fan ◽  
Pengtao Xu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Short Chain Fatty Acids ◽  
Antibiotic Exposure ◽  
Male Mice ◽  
Female Mice ◽  
Structural Composition ◽  
Host Metabolism

ABSTRACT The gut microbiota has the capability to regulate homeostasis of the host metabolism. Since antibiotic exposure can adversely affect the microbiome, we hypothesized that antibiotic effects on the gut microbiota and host metabolism are sex dependent. In this study, we examined the effects of antibiotic treatments, including vancomycin (Vanc) and ciprofloxacin-metronidazole (CiMe), on the gut microbiome and metabolome in colonic contents and tissues in both male and female mice. We found that the relative abundances and structural composition of Firmicutes were significantly reduced in female mice after both Vanc and CiMe treatments but in male mice only after treatment with Vanc. However, Vanc exposure considerably altered the relative abundances and structural composition of representatives of the Proteobacteria especially in male mice. The levels of short-chain fatty acids (SCFAs; acetate, butyrate, and propionate) in colonic contents and tissues were significantly decreased in female mice after both antibiotic treatments, while these reductions were detected in male mice only after Vanc treatment. However, another SCFA, formate, exhibited the opposite tendency in colonic tissues. Both antibiotic exposures significantly decreased the levels of alanine, branched-chain amino acids (BCAAs; leucine, isoleucine, and valine) and aromatic amino acids (AAAs; phenylalanine and tyrosine) in colonic contents of female mice but not in male mice. Additionally, female mice had much greater correlations between microbe and metabolite than male mice. These findings suggest that sex-dependent effects should be considered for antibiotic-induced modifications of the gut microbiota and host metabolism. IMPORTANCE Accumulating evidence shows that the gut microbiota regulates host metabolism by producing a series of metabolites, such as amino acids, bile acids, fatty acids, and others. These metabolites have a positive or negative effect on host health. Antibiotic exposure can disrupt the gut microbiota and thereby affect host metabolism and physiology. However, there are a limited number of studies addressing whether antibiotic effects on the gut microbiota and host metabolism are sex dependent. In this study, we uncovered a sex-dependent difference in antibiotic effects on the gut microbiota and metabolome in colonic contents and tissues in mice. These findings reveal that sex-dependent effects need to be considered for antibiotic use in scientific research or clinical practice. Moreover, this study will also give an important direction for future use of antibiotics to modify the gut microbiome and host metabolism in a sex-specific manner.

scholarly journals Novel Mechanisms in the Regulation of Phosphorus Homeostasis

Physiology ◽  
2009 ◽  
Vol 24 (1) ◽  
pp. 17-25 ◽  
Author(s):  
Theresa Berndt ◽  
Rajiv Kumar
Keyword(s):  
Critical Role ◽  
Endocrine System ◽  
Well Being ◽  
Inorganic Phosphorus ◽  
Biological Processes ◽  
Serum Concentrations ◽  
Short Term ◽  
Hormonal Factors ◽  
Fgf 23

Phosphorus plays a critical role in diverse biological processes, and, therefore, the regulation of phosphorus balance and homeostasis are critical to the well being of the organism. Changes in environmental, dietary, and serum concentrations of inorganic phosphorus are detected by sensors that elicit changes in cellular function and alter the efficiency by which phosphorus is conserved. Short-term, post-cibal responses that occur independently of hormones previously thought to be important in phosphorus homeostasis may play a larger role than previously appreciated in the regulation of phosphorus homeostasis. Several hormones and regulatory factors such as the vitamin D endocrine system, parathyroid hormone, and the phosphatonins (FGF-23, sFRP-4, MEPE) among others, may play a role only in the long-term regulation of phosphorus homeostasis. In this review, we discuss how organisms sense changes in phosphate concentrations and how changes in hormonal factors result in the conservation or excretion of phosphorus.

scholarly journals Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

2020 ◽  
Author(s):  
Travis T. Sims ◽  
Molly B. El Alam ◽  
Tatiana V. Karpinets ◽  
Stephanie Dorta-Estremera ◽  
Venkatesh L. Hegde ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Radiation Therapy ◽  
Gut Microbiota ◽  
Cancer Patients ◽  
Gut Microbiome ◽  
Compositional Variation ◽  
Short Term ◽  
Microbiome Diversity ◽  
Term Survivor

Diversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. The modulation of gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.

scholarly journals Structural changes in the gut microbiome of short-term and long-term medical workers compared to normal controls

2019 ◽  
Author(s):  
Ning Zheng ◽  
Shenghui Li ◽  
Bo Dong ◽  
Wen Sun ◽  
Huairui Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Structural Changes ◽  
Hospital Staff ◽  
Hospital Environment ◽  
Rrna Gene ◽  
Short Term ◽  
Normal Controls

ABSTRACTObjectiveHospital environment has been implicated in enrichment and exchange of pathogens and antibiotic resistances, but its potential in shaping the symbiotic microbial community of the hospital staff is unclear. This study was designed to evaluate the alteration of gut microbiome in medical workers compared to non-medical controls.DesignProspective cross-sectional cohort study.SettingIntensive care unit (ICU) and other departments from a center in northeast China.Subjects175 healthy medical workers (1-3 months short-term workers, n = 80; >1 year long-term workers, n = 95) and 80 healthy normal controls.InterventionsNone.Measurements and Main ResultsFecal samples of all subjects were analyzed using the 16S rRNA gene sequencing. Medical workers exhibited remarkable deviation in gut microbial within-sample diversity and enterotypes stratification, and shift in overall microbial structure. Short-term workers were significantly more abundant in taxa including Lactobacillus, Butyrivibrio, Clostridiaceae_Clostridium, Ruminococcus, Dialister, Bifidobacterium, Odoribacter and Desulfovibrio, and with lower abundances of Bacteroides and Blautia compared with the controls. While long-term workers were enriched in taxa including Dialister, Veillonella, Clostridiaceae_Clostridium, Bilophila, Desulfovibrio, Pseudomonas and Akkermansia, with lower abundances of Bacteroides and Coprococcus compared with the controls. In addition, medical worker’s working years (short-term vs. long-term), hospital department (resident doctor vs. nursing staff) and work position (ICU vs. not-ICU) revealed considerable effects on their gut microbiome. Moreover, by analyzing the environmental samples (n = 9) around the inpatient wards and the hospital, we showed that the gut microbiota of medical workers was closer to environmental microbiota than that of the normal controls, probably in correlation to lasting exposure to the pathogenic taxa (e.g. Pseudomonas) in health workers.ConclusionsOur findings demonstrated structural changes in the gut microbial community of the medical workers. Further studies are proposed for investigating the potentially physiological influence of the altered gut microbiome in medical participants.IMPORTANCEIn this study, we for the first time focused on the influence of hospital environmental factors on gut microbiota of medical workers. The significance of our study is not limited to revealing the remodeling effect of the hospital environment on the gut microbiota of medical workers. Based on these, we also propose targeted and operational recommendations that can promote the health of hospital staff.

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