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Gut Microbes

Pilar N Ossorio, Yao Zhou
In 2017 Gut Microbes published "A proposed definition of microbiota transplantation for regulatory purposes," in which the authors suggest that regulators should draw a line between microbiota transplants and biologic drugs composed of microbial communities (or other products derived from the human microbiome). They develop a definition of microbiota transplantation (MT) to help regulators draw such a line, and suggest that MT need not be, and cannot be, regulated as a biologic drug (a live biotherapeutic product)...
September 13, 2018: Gut Microbes
Chloe Matthews, Fiona Crispie, Eva Lewis, Michael Reid, Paul W O'Toole, Paul D Cotter
Methane is generated in the foregut of all ruminant animals by the microorganisms present. Dietary manipulation is regarded as the most effective and most convenient way to reduce methane emissions (and in turn energy loss in the animal) and increase nitrogen utilization efficiency. This review examines the impact of diet on bovine rumen function and outlines what is known about the rumen microbiome. Our understanding of this area has increased significantly in recent years due to the application of omics technologies to determine microbial composition and functionality patterns in the rumen...
September 12, 2018: Gut Microbes
Jennifer Lising Roxas, Gayatri Vedantam, V K Viswanathan
Desmosomes are junctional protein complexes that confer strong adhesive capacity to adjacent host cells. In a recent study, we showed that enteropathogenic Escherichia coli (EPEC) disrupts desmosomes, weakens cell-cell adhesion and perturbs barrier function of intestinal epithelial (C2BBe ) cells. Desmosomal damage was dependent on the EPEC effector protein EspH and its inhibitory effect on Rho GTPases. EspH-mediated Rho inactivation resulted in retraction of keratin intermediate filaments and degradation of desmosomal cadherins...
September 5, 2018: Gut Microbes
Christopher Strouse, Ashutosh Mangalam, Jun Zhang
The influence of the composition of the human microbiome on the efficacy of cancer directed immunotherapies, such as antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1), has garnered increasing attention as the role of immunotherapies in the care of cancer has grown. Dysbiosis (altered microbiota) has recently been reported to adversely affect the efficacy of cancer directed immunotherapies, and correction of this dysbiosis has the potential to improve the efficacy of these treatments...
September 5, 2018: Gut Microbes
Atsuo Nakamura, Takushi Ooga, Mitsuharu Matsumoto
The intestinal microbiome produces various metabolites that may harm or benefit the host. However, the production pathways of these metabolites have not been well characterised. The polyamines putrescine and spermidine required for physiological process are also produced by intestinal microbiome. The production and release of these polyamines by microbiome are poorly understood, though we have confirmed that intestinal bacteria produced putrescine from arginine. In this study, we characterised polyamine synthesis by analysing the collective metabolic functions of the intestinal microbiome...
September 5, 2018: Gut Microbes
Tanya Monaghan, Benjamin H Mullish, Jordan Patterson, Gane Ks Wong, Julian R Marchesi, Huiping Xu, Tahseen Jilani, Dina Kao
The mechanisms of efficacy for fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI) remain poorly defined, with restored gut microbiota-bile acid interactions representing one possible explanation. Furthermore, the potential implications for host physiology of these FMT-related changes in gut bile acid metabolism are also not well explored. In this study, we investigated the impact of FMT for rCDI upon signalling through the farnesoid X receptor (FXR)-fibroblast growth factor (FGF) pathway...
September 5, 2018: Gut Microbes
Fanli Kong, Feilong Deng, Ying Li, Jiangchao Zhao
The world population is aging, which poses a significant burden to the economy and health care system. As people age, so do their gut microbiomes. Age-related changes in gut microbiome have been reported, including decreased microbial diversity and increased Proteobacteria. Recently, we characterized the gut microbiome of a group of long-living (≥ 90 years old) Chinese people. Interestingly, the diversity of their gut microbiome was greater than that of a young adult control group. We also identified several potentially beneficial bacteria enriched in the long-living Chinese group...
August 24, 2018: Gut Microbes
Tomasz Cieplak, Nitzan Soffer, Alexander Sulakvelidze, Dennis Sandris Nielsen
Antibiotics offer an efficient means for managing diseases caused by bacterial pathogens. However, antibiotics are typically broad spectrum and they can indiscriminately kill beneficial microbes in body habitats such as the gut, deleteriously affecting the commensal gut microbiota. In addition, many bacteria have developed or are developing resistance to antibiotics, which complicates treatment and creates significant challenges in clinical medicine. Therefore, there is a real and urgent medical need to develop alternative antimicrobial approaches that will kill specific problem-causing bacteria without disturbing a normal, and often beneficial, gut microbiota...
August 24, 2018: Gut Microbes
Eugene B Chang, Kristina Martinez-Guryn
Our recently published paper "Small Intestine Microbiota Regulate Digestive and Absorptive Adaptive Responses to Dietary Lipids" in Cell Host & Microbe explored the neglected small intestine microbiota and demonstrated its critical role as a regulator of fat digestion and absorption. This work generated the following important take home messages: 1) small intestinal microbes are particularly sensitive to high fat diets and turn on host processes regulating fat digestion and transport, 2) this action is very likely orchestrated by a consortium of microbes, each having different specific effects and targets, and 3) the actions of this consortium appear to be mediated by bacteria-derived small molecules or bioactive components...
August 23, 2018: Gut Microbes
Fedja Farowski, Gregor Els, Anastasia Tsakmaklis, Paul G Higgins, Christian R Kahlert, Christoph K Stein-Thoeringer, Johanna S Bobardt, Katja Dettmer-Wilde, Peter J Oefner, Jörg Janne Vehreschild, Maria J G T Vehreschild
OBJECTIVES: After allogeneic hematopoietic stem cell transplantation (allo-HCT), urinary levels of 3-indoxyl sulfate (3-IS) correlate with the relative abundance of bacteria from the class Clostridia (RAC), and antibiotic treatment is considered the major determinant of this outcome. A high RAC has been associated with favorable outcome after allo-HCT and protection from Clostridium difficile infection (CDI). We assessed correlations between alpha diversity, RAC and urinary 3-IS levels in a non-allo-HCT clinical cohort of antibiotic treated patients to further explore 3-IS as a biomarker of reduced diversity and predisposition to CDI...
August 17, 2018: Gut Microbes
James Collins, Heather Danhof, Robert A Britton
In a recent study, we reported on two distantly related, epidemic lineages of Clostridium difficile that have acquired independent mechanisms to metabolize low concentrations of trehalose. Here we provide further comment and evidence that a third epidemic lineage common in Asia and Europe, ribotype 017, has evolved this ability.
August 17, 2018: Gut Microbes
Gabriela K Fragiadakis, Samuel A Smits, Erica D Sonnenburg, William Van Treuren, Gregor Reid, Rob Knight, Alphaxard Manjurano, John Changalucha, Maria Gloria Dominguez-Bello, Jeff Leach, Justin L Sonnenburg
The study of traditional populations provides a view of human-associated microbes unperturbed by industrialization, as well as a window into the microbiota that co-evolved with humans. Here we discuss our recent work characterizing the microbiota from the Hadza hunter-gatherers of Tanzania. We found seasonal shifts in bacterial taxa, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rare or absent from microbiotas of industrialized nations...
August 17, 2018: Gut Microbes
Tamaki Ito, Tsuyoshi Sekizuka, Norimi Kishi, Akifumi Yamashita, Makoto Kuroda
Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases such as obesity, diabetes, inflammatory bowel disease, and allergy. However, most intestinal bacteria are considered 'unculturable' bacteria, and their functions remain unknown. Although culture-independent genomic approaches have enabled us to gain insight into their potential roles, culture-based approaches are still required to understand their characteristic features and phenotypes...
August 17, 2018: Gut Microbes
Fatih Cakar, Franz G Zingl, Stefan Schild
Bacterial pathogens of the gastrointestinal tract alter their expression profile upon ingestion by the host and activate a variety of factors enhancing colonization and virulence. However, gene silencing during infection might be as important as gene activation to achieve full colonization fitness. Thus, we developed and successfully applied a reporter technology to identify 101 in vivo repressed (ivr) genes of the bacterial pathogen Vibrio cholerae. In depth analysis of the in vivo repressed H+ /Cl- transporter ClcA revealed an inverse requirement along gastrointestinal colonization...
August 15, 2018: Gut Microbes
Xu Han, Allen Lee, Sha Huang, Jun Gao, Jason R Spence, Chung Owyang
Disruption of intestinal barrier homeostasis is an important pathogenic factor in conditions such as irritable bowel syndrome (IBS). Lactobacillus rhamnosus GG (LGG) improves IBS symptoms through unclear mechanisms. Previous studies utilizing colorectal adenocarcinoma cell lines showed that LGG metabolites prevented interferon gamma (IFN-gamma) induced barrier damage but the model employed limited these findings. We aimed to interrogate the protective effects of LGG on epithelial barrier function using human intestinal epithelial cultures (enteroids and colonoids) as a more physiologic model...
July 24, 2018: Gut Microbes
Gloria Solano-Aguilar, Terez Shea-Donohue, Kathleen B Madden, Alejandro Quinoñes, Ethiopia Beshah, Sukla Lakshman, Yue Xie, Harry Dawson, Joseph F Urban
An evaluation of a localized intestinal allergic type-2 response concomitant with consumption of probiotic bacteria is not well documented. This study investigated the effect of feeding probiotic Bifidobacterium animalis subspecies lactis (Bb12) or a placebo in weaned pigs that were also inoculated with Ascaris suum (A. suum) eggs to induce a strong Th2-dependent allergic type 2 immune response. Sections of jejunal mucosa were mounted in Ussing chambers to determine changes in permeability and glucose absorption, intestine and liver samples were collected for analysis of type-2 related gene expression, jejunum examined histologically, and sera and intestinal fluid were assayed for parasite antigen specific antibody...
July 19, 2018: Gut Microbes
Luisa De Sordi, Marta Lourenço, Laurent Debarbieux
Viruses that infect bacteria, or bacteriophages, are among the most abundant entities in the gut microbiome. However, their role and the mechanisms by which they infect bacteria in the intestinal tract remain poorly understood. We recently reported that intestinal bacteria are an evolutionary force, driving the expansion of the bacteriophage host range by boosting the genetic variability of these viruses. Here, we expand these observations by studying antagonistic bacteriophage-bacteria coevolution dynamics and revealing that bacterial genetic variability is also increased under the pressure of bacteriophage predation...
June 18, 2018: Gut Microbes
Alexi A Schoenborn, Richard J von Furstenberg, Smrithi Valsaraj, Farah S Hussain, Molly Stein, Michael T Shanahan, Susan J Henning, Ajay S Gulati
Paneth cells (PCs) are epithelial cells found in the small intestine, next to intestinal stem cells (ISCs) at the base of the crypts. PCs secrete antimicrobial peptides (AMPs) that regulate the commensal gut microbiota. In contrast, little is known regarding how the enteric microbiota reciprocally influences PC function. In this study, we sought to characterize the impact of the enteric microbiota on PC biology in the mouse small intestine. This was done by first enumerating jejunal PCs in germ-free (GF) versus conventionally raised (CR) mice...
June 8, 2018: Gut Microbes
Deepika Bagga, Johanna Louise Reichert, Karl Koschutnig, Christoph Stefan Aigner, Peter Holzer, Kaisa Koskinen, Christine Moissl-Eichinger, Veronika Schöpf
Experimental manipulation of the gut microbiome was found to modify emotional and cognitive behavior, neurotransmitter expression and brain function in rodents, but corresponding human data remain scarce. The present double-blind, placebo-controlled randomised study aimed at investigating the effects of 4 weeks' probiotic administration on behavior, brain function and gut microbial composition in healthy volunteers. Forty-five healthy participants divided equally into three groups (probiotic, placebo and no intervention) underwent functional MRI (emotional decision-making and emotional recognition memory tasks)...
May 3, 2018: Gut Microbes
Anthony A Fodor, Mark Pimentel, William D Chey, Anthony Lembo, Pamela L Golden, Robert J Israel, Ian M Carroll
Rifaximin, a non-systemic antibiotic, is efficacious for the treatment of diarrhoea-predominant irritable bowel syndrome (IBS-D). Given the emerging association between the gut microbiota and IBS, this study examined potential effects of rifaximin on the gastrointestinal microbial community in patients with IBS-D. TARGET 3 was a randomised, double-blind, placebo-controlled, phase 3 study. Patients with IBS-D initially received open-label rifaximin 550 mg 3 times daily (TID) for 2 weeks. Patients who responded to the initial treatment and then relapsed were randomised to receive 2 repeat courses of rifaximin 550 mg TID or placebo for 2 weeks, with each course separated by 10 weeks...
April 30, 2018: Gut Microbes
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