Author Interviews, Microbiome / 19.05.2016

MedicalResearch.com Interview with: Martha Colin Founder of The BioCollectiveMartha Carlin Founder of The BioCollective MedicalResearch.com Editor’s Note: In recognition of the National Microbiome Initiative (NMI) announced by the White House Office of Science and Technology Policy, Martha Carlin, founder of the The BioCollective, discussed this research effort for the readers of MedicalResearch.com. ‘The BioCollective, is a direct-to-consumer microbiome marketplace where members receive a percentage of revenue from microbiome sample sales to scientists. By becoming a member of The BioCollective, individuals help advance microbiome research and learn about their own microbiome along the way.’  MedicalResearch.com: Would you tell us a little about yourself? How did you become interested in microbiomes? Martha Carlin: My husband was diagnosed with Parkinson’s Disease (PD) in 2002. At the time, John was 44 years old, a marathon runner and life-long athlete. He had always been healthy. We were both perplexed by both his diagnosis and wanted to do everything we could to maintain his quality of life as well as hinder the progression of the disease. Although I did not have a scientific background, I began studying the many fields of science so that I could piece together my observations of his health and his life history in my search for answers. After reading Dr. Martin Blaser’s Missing Microbes in 2014, I later connected it to Dr. Filip Scheperjans’ research showing a correlation between the presence or absence of specific gut bacteria and symptoms in Parkinson’s Disease. This accelerated my research and led me to Dr. Jack Gilbert at the University of Chicago who later became one of my co-founders. I started working with Jack on sequencing samples and learning more about the field of microbiome research. From this work, we saw a need for samples to accelerate the research and founded The BioCollective with our third co-founder, Dr. Suzanne Vernon. MedicalResearch.com: Can you briefly explain what a microbiome is? Does it just refer to the organisms in our intestines or are there other microbiomes? Are microbiomes unique to an individual or a community? Martha Carlin: The microbiome is the sum total of microbial life in your body - the bacteria, archaea, fungi and viruses that call you home. There are 100 trillion microbial cells in your body, and they collectively can influence your health in profound ways. The possibilities in microbiome research are exciting. It has the potential to create technologies as revolutionary as probiotics to prevent obesity and allergies; “living” buildings that reduce the spread of viruses or allergens in schools and offices; personalized diets to treat depression; growth-promoting animal feed that eliminates the need for growth-promoting antibiotics; bacteria to reduce methane production in cows and flooded soils; plant-microbiome interactions that suppress disease and improve productivity, and bacterial cocktails that restore the health of damaged aquatic ecosystems ranging from streams to oceans.
Author Interviews, Gastrointestinal Disease, Microbiome, Transplantation / 16.05.2016

MedicalResearch.com Interview with: Dr. Sudarshan Paramsothy University of New South Wales Australia MedicalResearch.com: What is the background for this study? What are the main findings? Dr. Paramsothy: This study was conducted as there is strong evidence that the gastrointestinal microbiota play a critical role in the underlying pathogenesis of inflammatory bowel disease (IBD), but treatments to date primarily are focused on controlling the associated immune response. Attempts at therapeutic microbial manipulation in ulcerative colitis (UC) to date (antibiotics, probiotics, prebiotics) have not been as impressive as one might expect. We felt intensive fecal microbiota transplantation (FMT) may be more successful than these other methods, as it involves transplanting the entire gastrointestinal microbiota from a health individual, and thus more likely to correct any underlying microbial disturbance or dysbiosis in the recipient UC patient. Our study found that significantly more active ulcerative colitis patients treated with intensive FMT than placebo (27% vs 8%) achieved the trial primary composite endpoint of both
  • clinical remission induction (ie resolution of symptoms) and
  • endoscopic remission or response (ie either healing or significant improvement of the bowel lining)
Author Interviews, Gastrointestinal Disease, Microbiome, Nature, Technology / 12.05.2016

MedicalResearch.com Interview with: [caption id="attachment_24295" align="alignleft" width="180"]Paul Wilmes Paul Wilmes[/caption] Prof. Dr. Paul Wilmes Associate Professor Head of the Eco-Systems Biology Research Group Luxembourg Centre for Systems Biomedicine University of Luxembourg Luxembourg MedicalResearch.com: What is the background for this intestinal model? Dr. Wilmes: Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential. Widely used animal models exhibit limitations. Therefore, we set out to develop the HuMiX model which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal interface.
Author Interviews, Bipolar Disorder, Infections, Johns Hopkins, Mental Health Research, Microbiome, Schizophrenia / 05.05.2016

MedicalResearch.com Interview with: [caption id="attachment_24088" align="alignleft" width="120"]Emily G. Severance, Ph.D Stanley Division of Developmental Neurovirology Department of Pediatrics Johns Hopkins University School of Medicine Baltimore, MD Dr. Emily Severance[/caption] Emily G. Severance, Ph.D Stanley Division of Developmental Neurovirology Department of Pediatrics Johns Hopkins University School of Medicine Baltimore, MD  MedicalResearch.com: What is the background for this study? What are the main findings? Dr. Severance: This research stems in part from anecdotal dialogues that we had with people with psychiatric disorders and their families, and repeatedly the issue of yeast infections came up. We found that Candida overgrowth was more prevalent in people with mental illness compared to those without psychiatric disorders and the patterns that we observed occurred in a surprisingly sex-specific manner.  The levels of IgG antibodies directed against the Candida albicans were elevated in males with schizophrenia and bipolar disorder compared to controls. In females, there were no differences in antibody levels between these groups, but in women with mental illness who had high amounts of these antibodies, we found significant memory deficits compared to those without evidence of past infection.
Author Interviews, Microbiome, Nutrition, Pediatrics, Weight Research / 05.05.2016

MedicalResearch.com Interview with: [caption id="attachment_24069" align="alignleft" width="133"]Jacob (Jed) E. Friedman, Professor, Ph.D. Department of Pediatrics, Biochemistry & Molecular Genetics Director, NIH Center for Human Nutrition Research Metabolism Core Laboratory University of Colorado Anschutz Dr. Jed Friedman[/caption] Jacob (Jed) E. Friedman, Professor, Ph.D. Department of Pediatrics, Biochemistry & Molecular Genetics Director, NIH Center for Human Nutrition Research Metabolism Core Laboratory University of Colorado Anschutz MedicalResearch.com: What is the background for this study? What are the main findings? Response: Scientists have long established that children who are breastfed are less likely to be obese as adults, though they have yet to identify precisely how breastfeeding protects children against obesity. One likely reason is that children who are breastfed have different bacteria in their intestines than those who are formula fed. The study, published Monday in the American Journal of Clinical Nutrition examines the role of human milk hormones in the development of infants’ microbiome, a bacterial ecosystem in the digestive system that contributes to multiple facets of health. “This is the first study of its kind to suggest that hormones in human milk may play an important role in shaping a healthy infant microbiome,” said Bridget Young, co-first author and assistant professor of pediatric nutrition at CU Anschutz. “We’ve known for a long time that breast milk contributes to infant intestinal maturation and healthy growth. This study suggests that hormones in milk may be partly responsible for this positive impact through interactions with the infant’s developing microbiome.” Researchers found that levels of insulin and leptin in the breastmilk were positively associated with greater microbial diversity and families of bacteria in the infants’ stool. Insulin and leptin were associated with bacterial functions that help the intestine develop as a barrier against harmful toxins, which help prevent intestinal inflammation. By promoting a stronger intestinal barrier early in life, these hormones also may protect children from chronic low-grade inflammation, which can lead to a host of additional digestive problems and diseases. In addition, researchers found significant differences in the intestinal microbiome of breastfed infants who are born to mothers with obesity compared to those born to mothers of normal weight. Infants born to mothers with obesity showed a significant reduction in gammaproteobacteria, a pioneer species that aids in normal intestinal development and microbiome maturation. Gammaproteobacteria have been shown in mice and newborn infants to cause a healthy amount inflammation in their intestines, protecting them from inflammatory and autoimmune disorders later in life. The 2-week-old infants born to obese mothers in this study had a reduced number of gammaproteobacteria in the infant gut microbiome.
Author Interviews, Cancer Research, Inflammation, Microbiome, PLoS, UCLA / 15.04.2016

MedicalResearch.com Interview with: [caption id="attachment_23468" align="alignleft" width="96"]Robert H. Schiestl PhD Department of Environmental Health Sciences, Fielding School of Public Health, Department of Pathology Department of Radiation Oncology Geffen School of Medicine University of California Los Angeles, Los Angeles, California Dr. Robert Schiestl[/caption] Robert H. Schiestl PhD Department of Environmental Health Sciences, Fielding School of Public Health, Department of Pathology Department of Radiation Oncology Geffen School of Medicine University of California Los Angeles, Los Angeles, California Medical Research: What is the background for this study? What are the main findings? Dr. Schiestl: When we moved from Harvard to UCLA 13 years ago, after 6 years at UCLA our Atm mouse colony lived significantly 4 fold longer and the frequency of DNA deletions was 4.5 fold reduced and the latency of lymphoma 2.5 fold different. Ultimately we identified the reason behind this as a difference in the intestinal bacteria. The Atm deficient mice are hypersensitive to inflammation and the bacteria reduced inflammation. Then I isolated the most prevalent bacterium among the health beneficial bacteria and this bacterium by itself called Lactobacillus johnsonii 456 reduced genotoxicity and all markers of inflammation.
Author Interviews, Microbiome, Multiple Sclerosis / 05.04.2016

MedicalResearch.com Interview with: [caption id="attachment_23164" align="alignleft" width="85"]Professor JF Cryan PhD Department of Anatomy and Neuroscience APC Microbiome Institute University College Cork Cork, Ireland Prof. John Cryan[/caption] Professor JF Cryan PhD Department of Anatomy and Neuroscience APC Microbiome Institute University College Cork Cork, Ireland MedicalResearch.com: What is the background for this study? What are the main findings?  Prof. Cryan: Over the past decade there has been an ever growing body of preclinical studies that highlight an essential role of the gut microbiota in many aspects of physiology including and perhps most surprtisingly the brain . Germ-free animals are one useful approach used to establish causality in gut microbiota-brain relationships. This model has been extremely useful in establishing that the microbiota is essential for appropriate stress responsibility, anxiety-like behaviours, neurogenesis, blood-brain barrier function and microglia activity. From these findings we can see that there is a clear cut role for the microbiota in CNS developmental processes. Here we wanted to investigate using next generation sequencing, as we had done previously in the amygdala what impact life without microbes has on transcriptional regulation in the prefrontal cortex, a brain region essential in many aspects of emotional behaviour. What we uncovered from this was that there was a large number of dysregulated genes in germ-free animals that have a direct role in myelination. We found increased expression levels of genes that encode for structural proteins that are key in forming the myelin sheath. We followed up this finding with transmission electron microscopy to identify whether this marked increase in myelin related gene expression was functional at a structural level. What we found was germ-free myelinated axons in the prefrontal cortex were hypermyelinated (lower g-ratio), they had thicker myelin sheaths compared to conventionally raised mice. Additionally we also had germ-free colonized animals, animals that were born germ-free but have been colonized with a conventional microbiome early in life. These animals displayed no change in myelin related gene expression and appeared to be indistinguishable from the conventional animals. However, at the protein levels they appeared to have increased myelin protein like germ-free mice. This could be due to the fact that these mice were germ-free for at least 3 weeks of life and the hypermyelinated axons had already been established before colonization. Really this shows that we can still target the microbiota in later life that can have an impact of myelin gene regulation.
Addiction, Dental Research, Microbiome, NYU, Smoking / 30.03.2016

MedicalResearch.com Interview with: Jiyoung Ahn, PhD, RD, MS Associate Professor of Population Health Associate Director of Population Sciences, NYU Perlmutter Cancer Center  and Brandilyn Peters (post-doctoral fellow, lead author) NYU Langone School of Medicine MedicalResearch.com: What is the background for this study? What are the main findings? Response: Oral bacteria play important roles in oral health, and can influence the health of other body systems as well. We were interested in studying how cigarette smoking affects oral bacteria. To do this, we examined the oral bacteria in mouthwash samples from 112 current smokers, 571 former smokers, and 521 people who never smoked. We found that the mouth bacterial composition of current smokers differed dramatically from those who never smoked. However, the mouth bacterial composition of former smokers was similar to that of never smokers, suggesting that quitting can restore the oral bacteria back to a healthy state.
Author Interviews, Microbiome / 30.03.2016

MedicalResearch.com Interview with: [caption id="attachment_22982" align="alignleft" width="150"]Jonas Schluter, DPhil Memorial Sloan Kettering Cancer Center New York City Dr. Jonas Schluter[/caption] Jonas Schluter, DPhil Memorial Sloan Kettering Cancer Center New York City [caption id="attachment_22983" align="alignleft" width="95"]Kirstie McLoughlin Department of Zoology Oxford University Dr. Kirstie McLoughlin[/caption] Kirstie McLoughlin Department of Zoology Oxford University  MedicalResearch.com: What is the background for this study? What are the main findings? Response: Microbes in our guts perform many important functions for our health. Healthy individuals are inhabited by a complex microbial community. A less diverse community is often a sign of ill health, and can be accompanied by loss of beneficial functions that a normal microbial community provides for the host. We try to understand how such complex communities can persist – after all, competition between microbes could lead to the eradication of slow-growing, but helpful microbes. We built a computer model of the gut that allows us to simulate how the host can actively help such slow microbes, and thereby maintain a healthily diverse microbial community. We show that a mechanism by which the host can achieve such selection is via secretions that help slow growing microbes persist by sticking in place. We propose that the host can change microbiota composition by conveying increased adhesion to disadvantages microbes, for example using mucus molecules and the attached sugars such as fucose. We hypothesise that this might also help explain the secretion of vast amounts of immune system molecules such as immunoglobulin A – perhaps they are not only a way to harm, but also to help certain microbes by anchoring them to the mucus. Indeed, we demonstrate that the host can change the selective effect of increased adhesion by tuning the mucus secretion rate: from beneficial for the adhered microbes at low mucus flow to detrimental at high mucus secretion rates.
Author Interviews, Dermatology, Microbiome / 09.03.2016

MedicalResearch.com Interview with: [caption id="attachment_22536" align="alignleft" width="133"]Sophie Seite, PhD La-Roche-Possy Dermatological Laboratories Asnières, France Dr. Sophie Seite[/caption] Sophie Seite, PhD La-Roche-Posay Dermatological Laboratories Asnières, France MedicalResearch.com: What is the background for this study? What are the main findings? Dr. Seite: These studies were performed in order to confirm the previous results published by H. Kong et al showing that the skin microbiota of atopic dermatitis patients was less diversified and presented an overabundance of S. aureus in comparison to healthy subjects. Because each of us has a specific skin microbiota (huge inter-individual variation) we performed an intra-individual design protocol in order to compare the microbiome of a lesional skin area to those of a non-lesional adjacent area. This strategy showed that the skin diversity in AD patients was reduced in non-lesional area and even more in lesional area and that not only Staphylococcus aureus is overabundant but also Staphylococcus epidermidis and Staphylococcus haemolyticus. Furthermore, for the first time the effect of a topical treatment on the skin microbiome was evaluated. Prebiotic strategies using thermal spring water or biomass lysate of nonpathogenic bacteria demonstrated their efficiency for a long term management of AD patients through an action on the skin microbiome.
Author Interviews, Gastrointestinal Disease, Lancet, Microbiome, Pediatrics / 09.03.2016

MedicalResearch.com Interview with: Phillip I. Tarr, MD Melvin E. Carnahan MD Professor of Pediatrics Director, Pediatric Division of Gastroenterolgy and Nutrition Washington University in St Louis School of Medicine St Louis, MO 63110, USA MedicalResearch.com: What is the background for this study? What are the main findings?

Dr. Tarr: There is a longstanding belief that gut bacteria are relevant to the developing necrotising enterocolitis (NEC). We have established dysbiosis in the gut before NEC occurs, suggesting this ecological perturbation might be causal.

Abuse and Neglect, BMJ, Imperial College, Microbiome, OBGYNE / 23.02.2016

MedicalResearch.com Interview with: [caption id="attachment_21901" align="alignleft" width="214"]Dr. Aubrey Cunnington Faculty of Medicine, Department of Medicine Clinical Senior Lecturer Imperial College, London Dr. Aubrey Cunnington[/caption] Dr. Aubrey Cunnington Faculty of Medicine, Department of Medicine Clinical Senior Lecturer Imperial College, London Medical Research: What is the background for this study? What are the main findings? Dr. Cunnington: We noticed that increasing numbers of women who were having Caesarean section deliveries at our hospitals were requesting for their vaginal fluid to be swabbed onto their babies after birth – a process often termed “vaginal seeding”. The idea behind this, is that it transfers all the natural bacteria (microbiota) from the mother’s vagina to the baby. We know that early on in life, babies born by Caesarean section have different bacteria living on their bodies and in their guts to those of babies born by vaginal delivery. Some people think these differences in the microbiota may be responsible for differences in long-term health, although a causal link is unproven. The hope is that vaginal seeding might reduce the risk of the baby developing some diseases like obesity and asthma in the future. Unfortunately we are a long way from having the evidence to show that this is possible, and we do not know whether vaginal seeding is really safe. Babies born by elective Caesarean section are at lower risk of transfer of some potentially harmful bacteria and viruses from the birth canal, but these harmful bacteria and viruses could be transferred to the baby on a swab and potentially cause a devastating infection. MedicalResearch.com Editor's note:  'Vaginal Seeding' is also known as "microbirthing",   
Author Interviews, Microbiome, Nutrition, Pediatrics, Weight Research / 12.02.2016

MedicalResearch.com Interview with [caption id="attachment_21538" align="alignleft" width="103"]Tine Rask Licht, Professor Head of Research Group on Gut Microbiology and Immunology Technical University of Denmark National Food Institute Søborg Prof. Tine Rask Licht[/caption] Tine Rask Licht, Professor Head of Research Group on Gut Microbiology and Immunology Technical University of Denmark National Food Institute Søborg Medical Research: What is the background for this study? What are the main findings? Response:  During childhood, the intestinal microbiota is under establishment. This period thus represents a ’window’, where the microbiota is likely to be more susceptible to be affected by external factors such as diet. Currently, it is well known that breast feeding has a major impact on the microbiota of young infants, but only very few studies have addressed the effect of the ‘next step’ in diet exposure, represented by complementary feeding. We studied two cohorts of children, born to normal-weight and obese mothers, respectively, and mapped the composition of bacteria in their fecal microbiota at age 9 months and 18 months.  We found that at 9 months, the microbiota was clearly affected by the composition of the complementary diet, but not by maternal obesity.
Author Interviews, Microbiome, Nature, NYU, OBGYNE / 01.02.2016

MedicalResearch.com Interview with: [caption id="attachment_21187" align="alignleft" width="150"]Maria Dominguez-Bello, PhD Associate Professor, Department of Medicine, Division of Translational Medicine NYU Langone Medical Center Dr. Dominguez-Bello[/caption] Maria Dominguez-Bello, PhD Associate Professor, Department of Medicine, Division of Translational Medicine NYU Langone Medical Center and [caption id="attachment_21188" align="alignleft" width="150"]Jose Clemente, PhD Assistant Professor, Departments of Genetics and Genomic Sciences, and Medicine Icahn School of Medicine at Mount Sinai Dr. Jose Clemente[/caption] Jose Clemente, PhD Assistant Professor, Departments of Genetics and Genomic Sciences, and Medicine Icahn School of Medicine at Mount Sinai       Medical Research: What is the background for this study? What are the main findings? Response: Humans and animals are a composite of their own cells and microbes. But where they get their microbes from?  For mammals, labor and birth are major exposures to maternal vaginal bacteria, and infants are born already with a microbiota acquired from the mother. Mom’s birth canal is heavily colonized by bacteria that are highly related to milk: some will use milk components and become dominant during early development, an important window for maturation of the immune system, the intestine and the brain. Thus, the maternal vaginal microbiota is thought to be of high adaptive value for newborn mammals. Indeed, studies in mice confirm that microbes acquired at birth are important to develop adequate immune and metabolic responses, and the mature adult microbiome will continue to modulate host metabolism and immunity. Humans are the only mammals that interrupt the exposure to maternal vaginal microbiota, by delivering babies by Cesarean section. C-sections save lives of babies and moms, and they are estimated necessary in 10-15% of the cases. But most Western countries have rates above 30%, with the notable exception of the Scandinavian countries, Holland and Japan, which have excellent health systems and low maternal-infant mortality rates. Previous work by us an others has shown that infants born by C-section acquire different microbiota at birth, and those differences are sustained over time, altering the normal age-dependent maturation of the microbiome. The fundamental questions are then, can we restore the microbiota of Cesarean delivered babies? And if we can, does that reduce the associated disease risks? In relation to the first question, we present here the results of a pilot study in which infants born by Cesarean delivery were exposed to maternal vaginal fluids at birth. A total of 18 infants were recruited for the study. Seven of them were vaginally delivered, the remaining 11 were born by scheduled C-section. Among the C-section infants, 4 were exposed to maternal vaginal fluids at birth and 7 were not. We sampled all infants and their mothers for the first month of life across different body sites (oral, skin, anal, maternal vagina) and determined the microbiome composition on a total of over 1,500 samples.
Author Interviews, C. difficile, Hospital Acquired, Infections, Microbiome / 07.01.2016

[caption id="attachment_20480" align="alignleft" width="128"]Casey M. Theriot, Ph.D. Assistant Professor Infectious Disease College of Veterinary Medicine Department of Population Health and Pathobiology North Carolina State University Raleigh, NC 27607 Dr. Casey Theriot[/caption] MedicalResearch.com Interview with: Casey M. Theriot, Ph.D. Assistant Professor Infectious Disease College of Veterinary Medicine Department of Population Health and Pathobiology North Carolina State University Raleigh, NC 27607 Medical Research: What is the background for this study? What are the main findings? Dr. Theriot: This study is an extension of the work we did in 2014 in our Nature Communications paper (Theriot et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection, 2014). We really wanted to know how different antibiotics that varied in their mechanism of action altered the gut microbiota in different ways and also in turn how this altered the bile acids present in the small and large intestine of mice. Primary bile acids are made by the host and are further converted to secondary bile acids by members of the microbiota in the large intestine. We know from previous work that secondary bile acids can inhibit the growth of C. difficile, but no one has looked in depth at the bile acid makeup in the actual gut before in the context of C. difficile. In this study we show that specific antibiotics that significantly alter the large intestinal gut microbiota and deplete all secondary bile acids allow for C. difficile to grow without any inhibition. We also showed that C. difficile spores are always germinating in the small intestine, which means in order to prevent this pathogen from colonizing the gut, we will have to target the growth of the pathogen. Moving forward the focus will be on trying to repopulate the gut with bacteria that are capable of restoring the secondary bile acid pools in order to inhibit C. difficile.
Author Interviews, Infections, JAMA, Microbiome / 24.12.2015

[caption id="attachment_20276" align="alignleft" width="100"]Tara F Carr, MD Assistant Professor, Medicine and Otolaryngology Allergy and Immunology Fellowship Training Program Director Director, Adult Allergy Division of Pulmonary, Allergy, Critical Care and Sleep Medicine University of Arizona Tucson, AZ 85724 Dr.  Carr[/caption] MedicalResearch.com Interview with: Tara F Carr, MD Assistant Professor, Medicine and Otolaryngology Allergy and Immunology Fellowship Training Program Director Director, Adult Allergy Division of Pulmonary, Allergy, Critical Care and Sleep Medicine University of Arizona Tucson, AZ 85724 Medical Research: What is the background for this study? What are the main findings? Dr. Carr: Some patients with chronic rhinosinusitis continue to suffer from symptoms despite aggressive medical and surgical treatments. For these individuals, therapy is generally chosen based on bacterial culture results, and often includes the use of topical antibacterial rinses with a medication called mupirocin.  We found that if patients are still having problems after this treatment, the bacteria identified from repeated sinus cultures are very different than those usually expected, and in general more difficult to treat.
Author Interviews, Microbiome, Weight Research / 28.11.2015

MedicalResearch.com Interview with: Dr. Eran Elinav PhD Immunology Department and Prof. Eran Segal PhD Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot , Israel Medical Research: What is the background for this study? Response: Obesity and diabetes are rising epidemics, affecting a significant portion of the world’s population. Blood glucose levels are a major contributor to these epidemics, as they are associated with obesity and with risk to develop diabetes. Normalizing blood glucose can have highly beneficial effects on the health of individuals. Therefore, we decided to study the factors that affect blood glucose. Among these factors are the macro- and micronutrient content of the meal, a person’s lifestyle, medical state, and their microbiome. We then started collecting from participants these exact parameters, and studied their effect on blood glucose. We managed to successfully predict the blood glucose response of many people to many meals and to assign for people beneficial diets based on this prediction.
Author Interviews, Gastrointestinal Disease, Microbiome / 11.11.2015

[caption id="attachment_19265" align="alignleft" width="200"]Shannon D. Manning, Ph.D., M.P.H. Dept. of Microbiology and Molecular Genetics Michigan State University E. Lansing, MI 48824 Dr. Manning[/caption] MedicalResearch.com Interview with: Shannon D. Manning, Ph.D., M.P.H. Dept. of Microbiology and Molecular Genetics Michigan State University E. Lansing, MI 48824 Medical Research: What is the background for this study? What are the main findings? Dr. Manning: Diarrheal disease is a leading cause of morbidity and mortality in children under the age of five and is commonly caused by many different bacterial pathogens. We have observed that infection with four different bacterial pathogens (Salmonella, Shigella, Shiga toxin-producing E. coli, and Campylobacter) all induce the proliferation of a population of microbes, namely Escherichia, which are already present in the gut of healthy individuals.
Author Interviews, Cancer Research, Microbiome / 04.11.2015

MedicalResearch.com Interview with: Simba Gill Ph.D CEO, Evelo Therapeutics MedicalResearch: Evelo Therapeutics, a new company focuses on leveraging the power of the microbiome to develop novel therapies for cancer. Evelo is pioneering Oncobiotic™ therapeutics, a new modality in cancer therapy based on the cancer microbiome. Dr. Gill, CEO of  Evelo Therapeutics began his career at Celltech, focused on antibody research. Dr. Gill earned his Ph.D. from King’s College, London, and his MBA from INSEAD. Medical Research:  What is a microbiome? How do microbiomes play a role in health and disease? Dr. Gill: The microbiome is the collection of trillions of bacteria, funguses, viruses and other microbes that live on and within the human body. There are different clusters of microbes in different parts of the body, including the skin, mouth, large intestine, and vagina. Recently we have learned that our microbial populations shift depending on changes to an individual’s health and wellness. The makeup of one’s microbiome has a strong influence on one’s health, immune response, and metabolic state.
Author Interviews, C. difficile, Gastrointestinal Disease, Mayo Clinic, Microbiome, Transplantation / 22.10.2015

[caption id="attachment_18565" align="alignleft" width="125"]Dr. Sahil Khanna MBBS Assistant Professor of Medicine Mayo Clinic Dr. Sahil Khanna[/caption] MedicalResearch.com Interview with: Dr. Sahil Khanna MBBS Assistant Professor of Medicine Mayo Clinic Medical Research: What is the background for this study? What are the main findings? Response: C. difficile infection patients are at a high risk of complications such as treatment failure. Gut microbiota signatures associated with CDI have been described but it is unclear if differences in gut microbiota play a role in response to therapy. No studies have identified predictors of treatment failure and we aimed to identified gut microbiota signatures to predict response to treatment for primary C. difficile . While there were no clinical predictors of treatment response, there were increases in certain genera in patients with successful treatment response in the fecal samples at initial diagnosis compared to non-responders. A risk index built from this panel of microbes highly differentiated between patients based on response and ROC curve analysis showed that this risk index was a strong predictor of treatment response, with a high area under the curve of 0.83..
Author Interviews, Eating Disorders, Microbiome / 06.10.2015

Dr. Ian Carroll, PhD Professor of medicine UNC Center for Gastrointestinal Biology and DiseaseMedicalResearch.com Interview with: Dr. Ian Carroll, PhD Professor of medicine UNC Center for Gastrointestinal Biology and Disease  Medical Research: What is the background for this study? What are the main findings? Dr. Carroll: Anorexia nervosa (AN) is a severe psychiatric disorder characterized by extreme weight dysregulation and presents with high rates of comorbid anxiety.Anorexia nervosa carries the highest mortality rate of all psychiatric illnesses and relapse is frequent. Although a prime contributor, genetic factors do not fully account for the etiology ofAnorexia nervosa, and non-genetic factors that contribute to the onset and persistence of this disease warrant investigation. Compelling evidence that the intestinal microbiota regulates adiposity and metabolism, and more recently, anxiety behavior, provides a strong rationale for exploring the role of this complex microbial community in the onset, maintenance of, and recovery from Anorexia nervosa. Our study provides evidence of an intestinal dysbiosis in AN and an association between mood and the enteric microbiota in this patient population.
Author Interviews, BMJ, Heart Disease, Mediterranean Diet, Microbiome, Nutrition, Vegetarians / 29.09.2015

Prof. Danilo Ercolini, PhD Department of Agricultural Sciences University of Naples Federico II Portici - ItalyMedicalResearch.com Interview with: Prof. Danilo Ercolini, PhD Department of Agricultural Sciences University of Naples Federico II Portici - Italy Medical Research: What is the background for this study? What are the main findings? Prof. Ercolini: There is a thick body of literature showing that diet can significantly impact the gut microbiota and metabolome. In a recent study, negligible differences in gut microbiota and feca lshort-chain fatty acids (SCFA) were reported between habitual omnivores and vegans in the USA. In addition, Mediterranean diet is a recognized healthy dietary pattern but has not previously been related to the composition of the gut microbiota and related metabolome. That’s the background in short. Here we show how habitual vegetarian and vegan diets promote enrichment of fibre-degrading bacteria in the gut. Subjects who consume a Mediterranean diet rich in fruit, legumes and vegetables have higher levels of fecal short chain fatty acids, regardless of the diet type. Low adherence to the Mediterranean diet corresponds to an increase in urinary trimethylamine oxide levels, a potential risk factor for cardiovascular disease.
AHA Journals, Author Interviews, Gastrointestinal Disease, Heart Disease, Microbiome / 16.09.2015

Jingyuan Fu, Ph.D. Associate professor of genetics University Medical Center Groningen NetherlandsMedicalResearch.com Interview with: Jingyuan Fu, Ph.D. Associate professor of genetics University Medical Center Groningen Netherlands  Medical Research: What is the background for this study? What are the main findings? Dr. Jingyuan Fu: Abnormal blood lipid levels are important risk factors for cardiovascular diseases. Because of that, a common advice is to have a healthy lifestyle or take lipid-lowering drugs like statin to control the blood lipid level. However, the problem is only partially solved. Cardiovascular disease remains the No 1 cause of death globally, representing 31% of all global deaths.  The primary purpose of the study is to look for a new solution in humans’ gut. Over millions of years, microbes and humans have formed a truly symbiotic relationship. Human body contains 10 trillion bacteria, 10x more than human cells. They help digest food and train our immune systems. As less than 30% of bacteria in human gut can be cultured, we know very little how they are and what they do in our gut. With the state-of-art deep sequencing technology, we are now able to see who are there. The research questions would be how much effect these bacteria could affect the blood lipids levels and which bacteria play important role. No such an analysis was done in large-scale human population. Our study was the first to provide solid evidence for the associations between gut bacteria and blood lipids. Although we cannot conclude cause-effect relationship yet, it serves an important step in narrowing possible therapeutic targets.
Allergies, Asthma, Author Interviews, Microbiome, Pulmonary Disease / 28.08.2015

Rebecca Normansell MA MB BChir Cochrane Airways Population Health Research Institute St George’s, University of London MedicalResearch.com Interview with: Rebecca Normansell MA MB BChir Cochrane Airways Population Health Research Institute St George’s, University of London     Medical Research: What is the background for this study? Response: Asthma is a common, long-term, respiratory condition which affects over 300 million people worldwide. It is a burden not only for the individual with asthma but also for the health services that care for them and the wider economy, due to days lost from work and school. Asthma therapies aim to prevent attacks and improve symptoms by reducing airway constriction and inflammation, but they come with their own risks of side effects. For example, long-term high-dose inhaled corticosteroids have been associated with growth restriction in children and long-acting beta2-agonists as mono-therapy have been associated with increased risk of death in people with asthma. There is growing interest in developing novel treatments for asthma and one such treatment is specific allergen immunotherapy. Immunotherapy has the potential to be a useful approach for asthma as it is thought that for approximately half of people with asthma, allergies are an important trigger for their symptoms and attacks. Immunotherapy can be delivered by injection (subcutaneously) or under the tongue (sublingually) and aims to bring about immune tolerance. Immunotherapy has already been demonstrated to be effective in certain conditions, such as allergic rhinitis and wasp and bee sting allergy, but its effectiveness and safety in asthma is less clear. In fact, immunotherapy is not recommended at all for use in people with severe or uncontrolled asthma due to the risk of triggering a serious respiratory reaction. Medical Research: What are the main findings? Response: Our review looked for trials in which people with asthma who were given sublingual immunotherapy (SLIT) were compared with those given placebo, or who continued usual asthma care. We found 52 randomised controlled trials which met our inclusion criteria, allocating over 5,000 people to either SLIT or placebo/usual care. Most of the participants had mild asthma and were allergic to either house dust mite or pollen. Despite the large number of eligible trials we were only able to perform a limited meta-analysis. This is because most of the trials did not report the efficacy outcomes we were most interested in: exacerbations and quality of life. Asthma symptoms and medication use were both more frequently reported, but often using different, un-validated scales so we did not perform a meta-analysis for these outcomes. However, we were able to combine serious adverse event data from 22 trials involving 2560 participants and data for all adverse events from 19 trials including 1755 participants. SLIT did not appear to be associated with an increased risk of serious adverse events, although very few events were observed overall. SLIT was associated with a small increase in the risk of all adverse events, which in absolute terms equated to an increase from 222 per 1000 people in the control group to 327 per 1000 (95% confidence intervals 257 to 404). Importantly, many of these events were mild and transient local reactions and did not generally result in participants withdrawing from the trial.
Author Interviews, Mental Health Research, Microbiome / 26.08.2015

Keith A. Crandall, PhD Director - Computational Biology Institute George Washington University Innovation Hall Suite 305 Ashburn, VA 20147-2766MedicalResearch.com Interview with: Keith A. Crandall, PhD Director - Computational Biology Institute George Washington University Innovation Hall Suite 305 Ashburn, VA 20147-2766 Medical Research: What is the background for this study? What are the main findings? Dr. Crandall: We wanted to investigate whether or not there were significant differences in the microbiome (microbial composition) of patients with schizophrenia versus controls.  The other researchers have demonstrated a connection between microbiome diversity and brain development and behavior modulation associated with a variety of disorders.  Our initial study focuses on the oropharyngeal as a target for the microbiome characterization, but we have additional work relating to other microbiomes (e.g., gut) for which we are still in the process of analyzing the data.     Collected microbiome data from 16 individuals with schizophrenia and 16 controls (matched as best we could and corrected statistically for differences between the populations), we showed differences in the microbiome taxonomic diversity and functional diversity.  Specifically, we identified a significant increase in the number of metabolic pathways related to metabolite transport systems; whereas, carbohydrate and lipid pathways and energy metabolism were abundant in controls.
Allergies, Asthma, Author Interviews, Microbiome / 14.08.2015

Yvonne J. Huang, MD Assistant Professor, Division of Pulmonary & Critical Care Medicine University of Michigan Health System Ann Arbor, MI 48109-5642 MedicalResearch.com Interview with: Yvonne J. Huang, MD Assistant Professor, Division of Pulmonary & Critical Care Medicine University of Michigan Health System Ann Arbor, MI  48109-5642   Medical Research: What is the background for this study? Dr. Huang: Asthma is a disease with many different clinical manifestations, and it is likely that multiple mechanisms play a role in asthma. Understanding the biological processes that contribute to this heterogeneity is an important goal of current translational research in asthma. One hypothesis that dates back several decades is whether asthma, at least in some forms, is linked to chronic airway infection or colonization by particular species of bacteria.  Results of early investigations in this regard were mixed, in part due to reliance on less sensitive methods to detect bacterial infection, but a new spin on this hypothesis has emerged in recent years.   This stems from the technological advances that now enable one to molecularly profile all bacteria present in a sample, such as via sequence analysis of conserved bacterial genes (such as that for 16S ribosomal RNA). 16S rRNA-based methods are now commonly used to profile bacterial microbiota in a variety of human niches, including in studies of respiratory disease. Prior to our current study, a few investigations had shown that the lower respiratory microbiome in adult asthmatics differs in bacterial composition (i.e. the types and relative abundance of bacteria present), compared to healthy controls.   In a previous study of patients with mild-moderate asthma, we also had found that clinical features of asthma, such as bronchial hyper-responsiveness, were associated with increased abundance of specific bacterial groups.  However, whether similar relationships between clinical features and the  microbiome exist in severe asthma was unknown, which we addressed in the current study.
Author Interviews, Gastrointestinal Disease, Microbiome, PLoS / 10.07.2015

MedicalResearch.com Interview with: Mashkoor A.  Choudhry, PhD Professor of Surgery, Microbiology & Immunology Burn & Shock Trauma Research Institute Stritch School of Medicine Loyola University Chicago Health Sciences Division Maywood, IL 60153 Medical Research: What is the background for this study? What are the main findings? Dr. Choudhry: Intestine is the major reservoir of bacteria in the body. We observed that gut bacterial composition is altered after burn injury. We found that burn causes a significant increase in Enterobacteriaceae, a group of bacteria that has the potential to be harmful for the host. Dysbiosis of the healthy intestinal microbiome is associated with a number of inflammatory conditions.
Author Interviews, Microbiome, Weight Research / 30.06.2015

Dr. Karine Clément M.D., Ph.D. Assistant Professor, Nutrition Department Hotel-Dieu hospital ParisMedicalResearch.com Interview with: Prof. Karine Clément MD, PhD Director ICAN - Institute of Cardiometabolism And Nutrition Hôpital La Pitié-Salpêtrière, Paris www.ican.paris k.clement@ican-institute.org Medical Research: What is the background for this study? What are the main findings? Dr. Clément: Obesity, associated with insulin resistance, is a chronic inflammatory disease revealed by a moderate but long-term increase in the levels of inflammatory molecules in the blood. Our groups and others have shown that several organs such as adipose tissues, liver, pancreas and muscles are also sites of inflammation with accumulation of immune cells such as macrophages and lymphocytes. This low-grade inflammatory state perturbs the tissue biology and contributes to the development and/or maintenance of insulin resistance and diabetes. In addition our teams and others showed that the intestinal functions are altered in obesity such as sugar and lipid absorption of and enteroendocrine nutrient signaling to the whole body. Our teams showed modifications of immunity in the obese intestine, and particularly in the jejunum part where most of sugar and lipid absorption takes place. Obesity increases the absorptive surface of the intestine and the colonization of the epithelium by CD8αβ T lymphocytes not affecting tissue integrity, thus differing from IBD inflammation. The cytokines secreted by the CD8 T cells of obese, but not lean subjects, are able to inhibit insulin action in enterocytes. In these patients, the increase of intestinal CD8 T cell density correlates with sugar absorption capacity and with the level of obesity and associated complications such as liver disease (NASH – Non-Alcoholic SteatoHepatitis) and dyslipidemia.
Author Interviews, Infections, Microbiome, Urinary Tract Infections / 29.06.2015

MedicalResearch.com Interview with: Jeffrey P. Henderson, M.D., Ph.D. Assistant Professor of Medicine and Molecular Microbiology Center for Women's Infectious Diseases Research Division of Infectious Diseases and Robin Shields-Cutler, Ph.D Ph.D. Student, Molecular Microbiology and Microbial Pathogenesis Washington University School of Medicine St. Louis, Missouri Medical Research: What is the background for this study? Response: Increasing antibiotic resistance, together with an appreciation that many patients are particularly susceptible to recurrent Urinary Tract Infections UTIs following antibiotic therapy, motivated interest in the events that occur during early stages of UTI pathogenesis. Abundant evidence suggests that uropathogenic E.coli must obtain iron from human hosts in order to cause a clinical infection. Early in infection, human cells secrete a protein called siderocalin that is known to limit bacterial growth by sequestering iron. This protein is detectable in the urine of Urinary Tract Infections patients. Medical Research: What are the main findings? Response: We obtained urine from a diverse panel of healthy volunteers, inoculated them individually with a uropathogenic E.coli strain, and monitored growth in the presence and absence of a fixed amount of siderocalin. Siderocalin exhibited a remarkably wide range of activity between individuals. We traced this variation back to differences in urinary pH and to phenolic urinary metabolites. We could significantly facilitate siderocalin’s antibacterial activity in urine by alkalinizing it above 6.5 and adding phenolic metabolites. The metabolites that potentiate siderocalin’s antibacterial effect have been linked to dietary sources such as coffee, tea, and berries. Some of these compounds may further derive from the actions of gut microbes on dietary phenols. The functional basis for these compounds’ properties seems to arise from siderocalin’s ability to use them as molecular grips that chelate iron ions in a form that is difficult for bacteria to access. From the pathogen perspective, we found that enterobactin, a molecule secreted by E.coli, acts as a microbial countermeasure to urinary siderocalin. Adding a drug-like inhibitor to urine that blocks enterobactin biosynthesis greatly increased siderocalin’s antibacterial effect.