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Microbiome programming

Agus Firmansyah, Nalinee Chongviriyaphan, Drupadi Hs Dillon, Nguyen Cong Khan, Tatsuya Morita, Kraisid Tontisirin, Le Danh Tuyen, Weiping Wang, Jacques Bindels, Paul Deurenberg, Sherlin Ong, Jo Hautvast, Diederick Meyer, Elaine E Vaughan
Inulin-based prebiotics are non-digestible polysaccharides that influence the composition of the gut microbiota in infants and children, notably eliciting a bifidogenic effect with high short chain fatty acid levels. Inulin, a generic term that comprises β-(2,1)-linked linear fructans, is typically isolated from the chicory plant root, and derivatives such as oligofructose and long chain inulin appear to have different physiological properties. The first 1000 days of a child's life are increasingly recognized as a critical timeframe for health also into adulthood, whereby nutrition plays a key role...
December 2016: Asia Pacific Journal of Clinical Nutrition
Jordan S Mar, Brandon J LaMere, Din L Lin, Sophia Levan, Michelle Nazareth, Uma Mahadevan, Susan V Lynch
UNLABELLED: Significant gut microbiota heterogeneity exists among ulcerative colitis (UC) patients, though the clinical implications of this variance are unknown. We hypothesized that ethnically distinct UC patients exhibit discrete gut microbiotas with unique metabolic programming that differentially influence immune activity and clinical status. Using parallel 16S rRNA and internal transcribed spacer 2 sequencing of fecal samples (UC, 30; healthy, 13), we corroborated previous observations of UC-associated bacterial diversity depletion and demonstrated significant Saccharomycetales expansion as characteristic of UC gut dysbiosis...
2016: MBio
Krijn K Dijkstra, Paula Voabil, Ton N Schumacher, Emile E Voest
Importance: Checkpoint blockade therapy targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and the programmed cell death protein 1 pathways (PD-1/PD-L1) have achieved success in treating a number of malignancies. However, only a subset of patients responds to these therapies, and optimization of patient selection for treatment is imperative to avoid adverse effects without clinical benefit and keep costs manageable. Observations: The past few years have witnessed checkpoint inhibition becoming a first-line treatment option with US Food and Drug Administration approvals for various tumor types...
August 4, 2016: JAMA Oncology
Fabien Magne, Miguel L O'Ryan, Roberto Vidal, Mauricio Farfan
PURPOSE OF REVIEW: The gut microbiome is critical for human health, and its alteration is associated with intestinal, autoimmune and metabolic diseases. Numerous studies have focused on prevention or treatment of dysbiotic microbiome to reduce the risk or effect of these diseases. A key issue is to define the microbiome associated with the state of good health. The purpose of this review is to describe factors influencing the gut microbiome with special emphasis on contributions from Latin America...
October 2016: Current Opinion in Infectious Diseases
Mari Murakami, Paola Tognini, Yu Liu, Kristin L Eckel-Mahan, Pierre Baldi, Paolo Sassone-Corsi
The liver circadian clock is reprogrammed by nutritional challenge through the rewiring of specific transcriptional pathways. As the gut microbiota is tightly connected to host metabolism, whose coordination is governed by the circadian clock, we explored whether gut microbes influence circadian homeostasis and how they distally control the peripheral clock in the liver. Using fecal transplant procedures we reveal that, in response to high-fat diet, the gut microbiota drives PPARγ-mediated activation of newly oscillatory transcriptional programs in the liver...
September 2016: EMBO Reports
Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S McLean, Shibu Yooseph
Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest...
July 2016: PLoS Computational Biology
Umesh D Wankhade, Keshari M Thakali, Kartik Shankar
The consequences of excessive maternal weight and adiposity at conception for the offspring are now well recognized. Maternal obesity increases the risk of overweight and obesity even in children born with appropriate-for-gestational age (AGA) birth weights. Studies in animal models have employed both caloric excess and manipulation of macronutrients (especially high-fat) to mimic hypercaloric intake present in obesity. Findings from these studies show transmission of susceptibility to obesity, metabolic dysfunction, alterations in glucose homeostasis, hepatic steatosis, skeletal muscle metabolism and neuroendocrine changes in the offspring...
November 5, 2016: Molecular and Cellular Endocrinology
Orit Matcovitch-Natan, Deborah R Winter, Amir Giladi, Stephanie Vargas Aguilar, Amit Spinrad, Sandrine Sarrazin, Hila Ben-Yehuda, Eyal David, Fabiola Zelada González, Pierre Perrin, Hadas Keren-Shaul, Meital Gury, David Lara-Astaiso, Christoph A Thaiss, Merav Cohen, Keren Bahar Halpern, Kuti Baruch, Aleksandra Deczkowska, Erika Lorenzo-Vivas, Shalev Itzkovitz, Eran Elinav, Michael H Sieweke, Michal Schwartz, Ido Amit
Microglia, the resident myeloid cells of the central nervous system, play important roles in life-long brain maintenance and in pathology. Despite their importance, their regulatory dynamics during brain development have not been fully elucidated. Using genome-wide chromatin and expression profiling coupled with single-cell transcriptomic analysis throughout development, we found that microglia undergo three temporal stages of development in synchrony with the brain--early, pre-, and adult microglia--which are under distinct regulatory circuits...
August 19, 2016: Science
Daniel H Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu
There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets...
June 2016: PLoS Computational Biology
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No abstract text is available yet for this article.
June 2016: Annals of Intensive Care
Rochellys Diaz Heijtz
The human gastrointestinal tract harbors a diverse and complex community of microbes, termed gut microbiota, that normally assemble during the first postnatal years of life. This evolution-driven process has been shown to contribute to the developmental programming of epithelial barrier function, gut homeostasis, and angiogenesis, as well as the development and function of the immune system. Research over the last few years has revealed that the actions of the gut microbiota have much wider effects on host physiology and development than originally believed, including the modulation of brain development and behavior...
May 30, 2016: Seminars in Fetal & Neonatal Medicine
Sophie Leclercq, Paul Forsythe, John Bienenstock
Gut bacteria strongly influence our metabolic, endocrine, immune, and both peripheral and central nervous systems. Microbiota do this directly and indirectly through their components, shed and secreted, ranging from fermented and digested dietary and host products to functionally active neurotransmitters including serotonin, dopamine, and γ-aminobutyric acid. Depression has been associated with enhanced levels of proinflammatory biomarkers and abnormal responses to stress. Posttraumatic stress disorder (PTSD) appears to be marked in addition by low cortisol responses, and these factors seem to predict and predispose individuals to develop PTSD after a traumatic event...
April 2016: Canadian Journal of Psychiatry. Revue Canadienne de Psychiatrie
F Lan, N Zhang, E Gevaert, L Zhang, C Bachert
Allergic airway diseases are typically characterized by a type 2-biased inflammation. Multiple distinct viruses and bacteria have been detected in the airways. Recently, it has been confirmed that the microbiome of allergic individuals differs from that of healthy subjects, showing a close relationship with the type 2 response in allergic airway disease. In this review, we summarize the recent findings on the prevalence of viruses and bacteria in type 2-biased airway diseases and on the mechanisms employed by viruses and bacteria in propagating type 2 responses...
October 2016: Allergy
Anna Zamora-Kapoor, Ka'imi Sinclair
This study aims to examine the relationship between infant-feeding practices and American Indian infants' gut microbiome--laying the foundation of a research program aimed at identifying potential aetiologies of childhood obesity in this population. Previous studies have emphasised the high prevalence of obesity in American Indian infants, but its underlying causes remain unclear. We received funding from the University of Washington to examine attitudes towards breastfeeding and formula feeding in American Indian mothers, their dietary and physical activity habits and the yield, quality and diversity of their infants' gut microbiome...
March 2016: Breastfeeding Review: Professional Publication of the Nursing Mothers' Association of Australia
Rodney R Dietert
Through its role as gatekeeper and filter to the external world, the microbiome affects developmental programming of physiological systems including the immune system. In turn, the immune system must tolerate, personalize, and prune the microbiome. Immune and host barrier status in early life significantly effects everything from embryo viability and pregnancy duration to the likelihood of misregulated inflammation, and risk of noncommunicable diseases (NCDs). Since the programming of and interactions among the microbiome, the host defense barrier, and the immune system can affect inflammation-driven health risks across the lifespan, a systems biology-type understanding of these three biological components may be useful...
May 7, 2016: Reproductive Toxicology
Alexander Eng, Elhanan Borenstein
MOTIVATION: Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems' optimization, suggest a promising route for microbial community engineering with numerous medical, environmental and industrial applications. However, such applications are currently restricted in scale and often rely on mimicking or enhancing natural communities, calling for the development of tools for designing synthetic communities with specific, tailored, desired metabolic capacities...
July 1, 2016: Bioinformatics
Julia Oh, Allyson L Byrd, Morgan Park, Heidi H Kong, Julia A Segre
Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability...
May 5, 2016: Cell
Philipp Engel, Waldan K Kwong, Quinn McFrederick, Kirk E Anderson, Seth Michael Barribeau, James Angus Chandler, R Scott Cornman, Jacques Dainat, Joachim R de Miranda, Vincent Doublet, Olivier Emery, Jay D Evans, Laurent Farinelli, Michelle L Flenniken, Fredrik Granberg, Juris A Grasis, Laurent Gauthier, Juliette Hayer, Hauke Koch, Sarah Kocher, Vincent G Martinson, Nancy Moran, Monica Munoz-Torres, Irene Newton, Robert J Paxton, Eli Powell, Ben M Sadd, Paul Schmid-Hempel, Regula Schmid-Hempel, Se Jin Song, Ryan S Schwarz, Dennis vanEngelsdorp, Benjamin Dainat
As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear...
2016: MBio
Susan L Prescott
Early-life nutritional exposures are significant determinants of the development and future health of all organ systems. The dramatic rise in infant immune diseases, most notably allergy, indicates the specific vulnerability of the immune system to early environmental changes. Dietary changes are at the center of the emerging epigenetic paradigms that underpin the rise in many modern inflammatory and metabolic diseases. There is growing evidence that exposures in pregnancy and the early postnatal period can modify gene expression and disease susceptibility...
2016: Nestlé Nutrition Institute Workshop Series
Walter Alexander
Featured topics: benzhydrocodone, hydrocodone, and an opioid taper program at the American Academy of Pain Medicine; and disruption of the gut microbiome by drugs plus new approaches to depression at the Integrative Healthcare Symposium.
April 2016: P & T: a Peer-reviewed Journal for Formulary Management
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