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Trend Chart oN
MICROBIOTa
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contents
January 2019, 16th

FEATURE STORY
●  AllergoOncology: microbiota in allergy and cancer - an EAACI position paper
BASIC SCIENCE 
● The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients
● Effect of the nursing mother on the gut microbiome of the offspring during early mouse development
● Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway
DYSBIOSIS
●  Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis 
● Airway microenvironment alterations and pathogen growth in cystic fibrosis
●  Obesity aggravates acute pancreatitis via damaging intestinal mucosal barrier
HOMEOSTASIS - THERAPY
● Oral faecal microbiota transplantation for the treatment of Clostridium difficile-associated diarrhoea in a dog
CLINICAL TRIALS - DATA 
● Review of donor features, procedures and outcomes in 168 clinical studies of faecal microbiota transplantation
MISCELLANEOUS
● Bacteriophages in food applications
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FEATURE STORY
AllergoOncology: microbiota in allergy and cancer - an EAACI position paper
The microbiota can play important roles in the development of human immunity and the establishment of immune homeostasis. Lifestyle factors including diet, hygiene, and exposure to viruses or bacteria, and medical interventions with antibiotics or anti-ulcer medications, regulate phylogenetic variability and the quality of cross-talk between innate and adaptive immune cells via mucosal and skin epithelia. More recently, microbiota and their composition have been linked to protective effects for health. Imbalance, however, has been linked to immune-related diseases such as allergy and cancer, characterized by impaired, or exaggerated immune tolerance, respectively. In this AllergoOncology position paper, researchers focus on the increasing evidence defining the microbiota composition as a key determinant of immunity and immune tolerance, linked to the risk for development of allergic and malignant diseases.
The position paper appeared in January 12th online issue of Allergy 
Related Informations/Publications
-Microorganisms. 2019 Jan 10;7(1). pii: E14. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Rinninella E et al. Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
Results / Comments: Understanding the cause or consequence of these gut microbiota balances in health and disease and how to maintain or restore a healthy gut microbiota composition should be useful in developing promising therapeutic interventions. Link: Abstract  - Full Text 
-Crit Rev Food Sci Nutr. 2019 Jan 11:1-13. Targeting gut microbiota with dietary components on cancer: Effects and potential mechanisms of action. Tao J et al. School of Public Health , Sun Yat-Sen University , Guangzhou , China. Link: Abstract  
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BASIC SCIENCE
The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients
Dutch researchers initiated the 1000IBD project to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, they have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing. The review appeared in January 08th online issue of BMC Gastroenterol (Abstract - Full Text)
Related Informations / Publications
-Semin Perinatol. 2018 Nov;42(7):425-431. Genomics, microbiomics, proteomics, and metabolomics in bronchopulmonary dysplasia. Lal CV et al. University of Alabama at Birmingham, USA. Link: Abstract
-Nat Methods. 2018 Oct;15(10):796-798. Qiita: rapid, web-enabled microbiome meta-analysis. Gonzalez A et al. University of California, San Diego, La Jolla, CA, USA. Link: Abstract 
-Front Microbiol
. 2018 Mar 1;9:365. BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data. McNally CP et al. University of Washington, Seattle, WA, USA
Results / Comments : Researchers describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes. Link : Abstract - Full Text
Effect of the nursing mother on the gut microbiome of the offspring during early mouse development
The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response.
The results appeared in January 10th online issue of Microb Ecol.
Related Informations / Publications
-Front Microbiol. 2018 Dec 18;9:3138. Dynamics of Gut Microbiome in Giant Panda Cubs Reveal Transitional Microbes and Pathways in Early Life. Guo M et al. University of Macau, Macau, China. Link: Abstract - Full Text 
-Yale J Biol Med. 2018 Dec 21;91(4):445-455. Natural Selection, The Microbiome, and Public Health. Swain Ewald HA et al. Department of Biology, University of Louisville, Louisville, KY, USA. Link: Abstract - Full Text 
-Birth Defects Res. 2018 Dec 1;110(20):1494-1503. Inherited nongenetic influences on the gut microbiome and immune system. Knoop KA et al. Results/Comments. The researchers here discuss how these nongenetic maternal influences can have long-term effects on the progeny's health
Link: Abstract - Full Text 
Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway
The importance of gut microbiota in human health and pathophysiology is undisputable. Despite the abundance of metagenomics data, the functional dynamics of gut microbiota in human health and disease remain elusive. Urolithin A (UroA), a major microbial metabolite derived from polyphenolics of berries and pomegranate fruits displays anti-inflammatory, anti-oxidative, and anti-ageing activities. Researchers now show that UroA and its potent synthetic analogue (UAS03) significantly enhance gut barrier function and inhibit unwarranted inflammation. They demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2–related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. Importantly, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction in addition to anti-inflammatory activities. The results appeared in January 09th online issue of Nat Comm
Related Informations / Publications
-Mol Nutr Food Res. 2018 Jun;62(11):e1800160. The Endotoxemia Marker Lipopolysaccharide-Binding Protein is Reduced in Overweight-Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial. González-Sarrías A et al. CEBAS-CSIC, P.O. Box 164, 30100, Campus de Espinardo, Murcia, Spain
Results/Comments: Consumption of pomegranate extracts decreased endotoxemia in overweight-obese individuals by reshaping the gut microbiota, mainly through the modulation of Faecalibacterium, Odoribacter, and Parvimonas. Link:  Abstract 
¬Food Funct. 2018 May 23;9(5):2617-2622. Consumption of pomegranate decreases plasma lipopolysaccharide-binding protein levels, a marker of metabolic endotoxemia, in patients with newly diagnosed colorectal cancer: a randomized controlled clinical trial. González-Sarrías A et al. CEBAS-CSIC, P.O. Box 164, 30100, Campus de Espinardo, Murcia, Spain. Link: Abstract 
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DYSBIOSIS
Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis
Clostridium difficile infection (CDI) is a major public health threat worldwide. The use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with enhanced susceptibility to and severity of CDI; however, the mechanisms driving this phenomenon have not been elucidated. NSAIDs alter prostaglandin (PG) metabolism by inhibiting cyclooxygenase (COX) enzymes. Americain researchers now found that treatment with the NSAID indomethacin prior to infection altered the microbiota and dramatically increased mortality and the intestinal pathology associated with CDI in mice. They now demonstrated that in C. difficile-infected animals, indomethacin treatment led to PG deregulation, an altered proinflammatory transcriptional and protein profile, and perturbed epithelial cell junctions. These effects were paralleled by increased recruitment of intestinal neutrophils and CD4+ cells and also by a perturbation of the gut microbiota.
The results appeared in January 8th online issue of MBio.
Related Informations / Publications
-Front Microbiol. 2018 Dec 21;9:2976. Bacteroides fragilis Prevents Clostridium difficile Infection in a Mouse Model by Restoring Gut Barrier and Microbiome Regulation. Deng H et al. Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Results/Comments: This study provides an alternative preventative measure for CDI and lays the foundations for further investigations of the relationships among opportunistic pathogens, commensal microbiota, and the gut barrier. Link: Abstract - Full Text 
-Acta Microbiol Immunol Hung. 2018 Dec 26:1-10. Experiences with fecal microbiota transplantation in Clostridium difficile infections via upper gastrointestinal tract. Vigvári S et al. University of Pécs , Pécs, Hungary.
Link: Abstract 
Airway microenvironment alterations and pathogen growth in cystic fibrosis
Cystic Fibrosis Transmembrane Regulator (CFTR) dysfunction is associated with epithelial cell vulnerability and with dysregulation of the local inflammatory responses resulting in excessive airway neutrophilic inflammation and pathogen growth. In combination with impaired mucociliary clearance, and dysregulation of defense function, bacterial infection follows with eventual airway damage and remodeling. Because of these inherent vulnerabilities, viral infections are also more severe and prolonged and appear to render the airway even more prone to bacterial infection. Airway acidity, deficient nitric oxide production and increased iron concentrations, further enhance the airway milieu's susceptibility to infection. Novel diagnostic techniques of the airway microbiome elucidate the coexistence of an array of non-virulent taxa beyond the recognized virulent organisms, predominantly Pseudomonas aeruginosa. The complex interplay between these two bacterial populations, including upregulation of virulence genes and utilization of mucin as a nutrient source, modulates the action of pathogens, modifies the CF airway milieu and contributes to the processes leading to airway derangement. The review provides an update on recent advances of the complex mechanisms that render the CF airway vulnerable to inflammation, infection and ultimately structural damage, the key pathogenetic elements of CF.
The results appeared in January online issue of Pediatr Pulmonol.
Related Informations / Publications
-J Cyst Fibros. 2018 Dec 20. Differences in the lower airway microbiota of infants with and without cystic fibrosis. Frayman KB et al. Murdoch Childrens Research Institute, Victoria, Australia; Department of Paediatrics, University of Melbourne, Victoria, Australia.
Results/Comments: In CF lung disease, differences in lower airway microbial community composition and structure are established by age 6-months.
Link: Abstract
-Yale University (US). Microbiome Acquisition and Progression of Inflammation and Airway Disease in Infants and Children With Cystic Fibrosis. Estimated Enrollment : 60. Updated : January 9th, 2019.
Link: NCT01661491 
Obesity aggravates acute pancreatitis via damaging intestinal mucosal barrier
Obesity may aggravate acute pancreatitis (AP) through damaging the intestinal mucosal barrier (IMB). The underlying mechanism remains unclear. This study was aimed to provide further data to clarify the mechanism. 48 rats were divided into 4 groups: 1) normal control (NC), chow-fed rats with sham operation, 2) no-obese rats with AP (NAP), chow-fed rats with taurocholate infusion, 3) obese control (OC), high-fat diet (HFD)-fed rats with sham operation, and 4) obese rats with AP (OAP), HFD-fed rats with taurocholate infusion. The study concludes that obesity may result in decreased intestinal leptin/ObR-b binding, distinct phylogenetic clusters of ileal bacterial communities, increased intestinal inflammatory injury and the insufficient intestinal epithelial cells proliferation during AP attack.
The results appeared in January 11th online issue of Sci Rep.
Related Informations / Publications
-Mol Nutr Food Res. 2019 Jan 12:e1800870. Sex differences in the gut microbiota as potential determinants of gender predisposition to disease. Santos-Marcos JA et al. Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain.
Results/Comments: The results suggest the potential involvement of differences in gut microbiota in the unequal incidence of metabolic diseases between genders, and a sex-dependent effect on shaping the gut microbiota according to diet. Link: Abstract 
-Sci Rep. 2019 Jan 11;9(1):67. The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome. Pak HH et al. William S. Middleton Memorial Veterans Hospital, Madison, WI, USA. Link: Abstract - Full Text
-Mediators Inflamm. 2018 Dec 9;2018:2037838. Gut Microbiome Dysbiosis and Immunometabolism: New Frontiers for Treatment of Metabolic Diseases. Belizário JE et al. Institute of Biomedical Sciences, University of São Paulo, SP CEP 05508-900, Brazil. Link: Abstract - Full Text 
-Front Microbiol. 2018 Dec 10;9:3045. Gut Microbiota Is a Major Contributor to Adiposity in Pigs. Yang H et al. Zhejiang Academy of Agricultural Sciences, Hangzhou, China. Link: Abstract - Full Text
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HOMeostasis - therapy
Oral faecal microbiota transplantation for the treatment of Clostridium difficile-associated diarrhoea in a dog
In this study, an 8-month-old, intact male French bulldog was presented with a 4-month history of intermittent large bowel diarrhoea. Physical and clinical examinations did not identify any specific causes for diarrhoea. Real-time PCR analysis and immunochromatography detected C. difficile antigen and toxin A&B genes and proteins in a faecal sample. Based on these findings, diarrhoea in the dog was considered to be induced by C. difficile-associated colitis. The dog was treated with oral FMT, in which a faecal solution obtained from a healthy beagle was orally administered to the subject. Stool consistency and frequency and faecal blood and mucus became normal 2-3 days after oral FMT, and real-time PCR analysis and immunochromatography was negative for C. difficile antigen and toxin A&B genes and proteins. No adverse events were observed.
The results appeared in January 07th online issue of BMC Vet Res.
Related Informations / Publications
-Clin Microbiol Infect. 2019 Jan 4. A five-day course of oral antibiotics followed by faecal transplantation to eradicate carriage of multidrug-resistant Enterobacteriaceae: A Randomized Clinical Trial. Huttner BD et al. Geneva University Hospitals, Geneva, Switzerland
Results/Comments: Non-absorbable antibiotics followed by FMT slightly decreased ESBL/CPE carriage compared to controls; this difference was not statistically significant, potentially due to early trial-termination. Further clinical investigations seem warranted. Link: Abstract 
-Gastroenterology. 2019 Jan 2. pii: S0016-5085(18)35434-9. Fecal Microbiota Transplantation is Superior to Fidaxomicin for Treatment of Recurrent Clostridium difficile Infection. Hvas CL et al. Aarhus University Hospital, Aarhus, Denmark
Results/Comments: In a randomized trial of patients with rCDI, we found the combination of vancomycin and FMT to be superior to fidaxomicin or vancomycin, based on endpoints of clinical and microbiological resolution or clinical resolution alone (NCT02743234). Link : Abstract - Full Text
-World J Clin Cases. 2018 Dec 26;6(16):1121-1127. Safety of fecal microbiota transplantation in Chinese children: A single-center retrospective study. Wang XY et al. Shanghai Jiao Tong University, Shanghai 200040, China.
Results/Comments: Although FMT was proven to be tolerated in children, we need to be more cautious with immunodeficient patients. The effect on children's long-term health is unpredictable Link: Abstract - Full Text
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CLINICAL TRIALS - DATA
Review of donor features, procedures and outcomes in 168 clinical studies of faecal microbiota transplantation
Chinese researchers systematically reviewed FMT studies published up to 29 August 2018 using MEDLINE (R) and EMBASE and identified clinical studies with FMT donor information. They reported data on donor characteristics, screening criteria, administration, clinical outcomes and adverse events. Among 5267 reports, 239 full-text articles were screened and 168 articles were included. FMT was performed commonly for Clostridium difficile infections CDI (n=108) and inflammatory bowel disease (IBD, https://www.mayoclinic.org/diseases-conditions/inflammatory-bowel-disease/symptoms-causes/syc-20353315) (n= 1). They reported characteristics of 1513 donors [58% male; mean age, 34.3 years; mean body mass index, 21.6]. Donors in Asia were younger than the West (mean age 30.7 vs 32.9, P=0.00075). Less than 50% of studies screened donors for transmittable pathogens. Final cure rate for CDI was 95.6% (95% confidence interval [CI], 93.9%-97.1%) and final remission rates for ulcerative colitis (UC) and Crohn's disease (CD) were 39.6% (95% CI, 25.4%-54.6%) and 47.5% (95% CI, 29.4%-65.8%), respectively. Cure rates in CDI and final remission rates for CD and UC were comparable across all routes of FMT administration. Overall adverse event incidence was <1%, mostly GI-related. Adverse event rates did not differ significantly between routes of FMT administration or indication.
The review appeared in January 09th online issue of Aliment Pharmacol Ther. AbstractFull Text 
Related Informations / Publications
-Biomed Res Int. 2018 Sep 13;2018:8941340. Protocol for Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis. Fang H et al. The Second Hospital of Anhui Medical University, Hefei, Anhui Province, China. Link: Abstract  - Full Text
-Crit Rev Food Sci Nutr. 2018 Dec 30:1-13. Efficacy of synbiotic supplementation in obesity treatment: A systematic review and meta-analysis of clinical trials. Hadi L et al. Isfahan University of Medical Sciences , Isfahan , Iran.
Results/Comments: Modulation of gut microbiota composition through synbiotic supplementation might have modest effects on body weight and waist circumference. Link: Abstract 
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miscellaneous
Bacteriophages in food applications
Bacteriophages (phages) have traditionally been considered troublesome in food fermentations, as they are an important cause of starter-culture failure and trigger significant financial losses. In addition, from an evolutionary perspective, phages have contributed to the pathogenicity of many bacteria through transduction of virulence genes. In contrast, phages have played an important positive role in molecular biology. Moreover, these agents are increasingly being recognized as a potential solution to the detection and biocontrol of various undesirable bacteria, which cause either spoilage of food materials, decreased microbiological safety of foods, or infectious diseases in food animals and crops. The documented successful applications of phages and various phage-derived molecules are discussed in this review, as are many promising new uses that are currently under development.
The analysis appeared in January 11th online issue of Annu Rev Food Sci Technol.
Related Informations / Publications
-Microbiol Mol Biol Rev. 2019 Jan 9;83(1). Cross-Domain and Viral Interactions in the Microbiome. Rowan-Nash AD et al. Brown University, Providence, Rhode Island, USA.
Link: Abstract
-Viruses. 2018 Dec 25;11(1). Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Van Belleghem JD et al. Ghent University, 9000 Ghent, Belgium
Results/Comments: The researchers here present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions Link: Abstract 
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