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Gut biome

Harald Brüssow
The gut microbiome research is going from a descriptive into an intervention phase. To optimize beneficial microbe-host interaction, we need to understand how to steer the system by modulating the nutrient input with which the system is literally fed (e.g. diets, fibres, prebiotics, human milk oligosaccharides), and we must learn how to modulate the composition of the gut microbiota by adding beneficial microbes (e.g. probiotics, faecal transplants) and by eliminating disturbing microbial members using, for example, bacteriophages in this highly complex ecosystem...
September 2016: Microbial Biotechnology
Mark L Heiman, Frank L Greenway
BACKGROUND: Like all healthy ecosystems, richness of microbiota species characterizes the GI microbiome in healthy individuals. Conversely, a loss in species diversity is a common finding in several disease states. This biome is flooded with energy in the form of undigested and partially digested foods, and in some cases drugs and dietary supplements. Each microbiotic species in the biome transforms that energy into new molecules, which may signal messages to physiological systems of the host...
May 2016: Molecular Metabolism
Sabina Górska, Petra Hermanova, Jarosław Ciekot, Martin Schwarzer, Dagmar Srutkova, Ewa Brzozowska, Hana Kozakova, Andrzej Gamian
The ITALIC! Lactobacillus caseistrain, LOCK 0919, is intended for the dietary management of food allergies and atopic dermatitis (LATOPIC(®)BIOMED). The use of a probiotic to modulate immune responses is an interesting strategy for solving imbalance problems of gut microflora that may lead to various disorders. However, the exact bacterial signaling mechanisms underlying such modulations are still far from being understood. Here, we investigated variations in the chemical compositions and immunomodulatory properties of the polysaccharides (PS), L919/A and L919/B, which are produced by ITALIC! L...
April 21, 2016: Glycobiology
Hirokazu Toju, Satoshi Yamamoto, Akifumi S Tanabe, Takashi Hayakawa, Hiroshi S Ishii
Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population...
March 2016: Journal of the Royal Society, Interface
Guillermo Blanco, Carolina Bravo, Erica C Pacifico, Daniel Chamorro, Karina L Speziale, Sergio A Lambertucci, Fernando Hiraldo, José L Tella
Despite the fact that parrots (Psitacifformes) are generalist apex frugivores, they have largely been considered plant antagonists and thus neglected as seed dispersers of their food plants. Internal dispersal was investigated by searching for seeds in faeces opportunistically collected at communal roosts, foraging sites and nests of eleven parrot species in different habitats and biomes in the Neotropics. Multiple intact seeds of seven plant species of five families were found in a variable proportion of faeces from four parrot species...
2016: PeerJ
Mark Obrenovich, Rudolf Flückiger, Lorraine Sykes, Curtis Donskey
We know that within the complex mammalian gut is any number of metabolic biomes. The gut has been sometimes called the "second brain" within the "gut-brain axis". A more informative term would be the gut-brain metabolic interactome, which is coined here to underscore the relationship between the digestive system and cognitive function or dysfunction as the case may be. Co-metabolism between the host and the intestinal microbiota is essential for life's processes. How diet, lifestyle, antibiotics and other factors shape the gut microbiome constitutes a rapidly growing area of research...
2016: CNS & Neurological Disorders Drug Targets
Gabriel A Al-Ghalith, Emmanuel Montassier, Henry N Ward, Dan Knights
The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs)...
January 2016: PLoS Computational Biology
Bruno R Fermino, Fernando Paiva, Priscilla Soares, Luiz Eduardo R Tavares, Laerte B Viola, Robson C Ferreira, Robinson Botero-Arias, Cátia D de-Paula, Marta Campaner, Carmen S A Takata, Marta M G Teixeira, Erney P Camargo
Trypanosoma terena and Trypanosoma ralphi are known species of the South American crocodilians Caiman crocodilus, Caiman yacare and Melanosuchus niger and are phylogenetically related to the tsetse-transmitted Trypanosoma grayi of the African Crocodylus niloticus. These trypanosomes form the Crocodilian clade of the terrestrial clade of the genus Trypanosoma. A PCR-survey for trypanosomes in caiman blood samples and in leeches taken from caimans revealed unknown trypanosome diversity and frequent mixed infections...
December 2015: International Journal for Parasitology. Parasites and Wildlife
Alain Brauman, Muhammad Zeeshan Majeed, Bruno Buatois, Alain Robert, Anne-Laure Pablo, Edouard Miambi
In the tropics, termites are major players in the mineralization of organic matter leading to the production of greenhouse gases including nitrous oxide (N2O). Termites have a wide trophic diversity and their N-metabolism depends on the feeding guild. This study assessed the extent to which N2O emission levels were determined by termite feeding guild and tested the hypothesis that termite species feeding on a diet rich in N emit higher levels of N2O than those feeding on a diet low in N. An in-vitro incubation approach was used to determine the levels of N2O production in 14 termite species belonging to different feeding guilds, collected from a wide range of biomes...
2015: PloS One
Gregory Ditzler, J Calvin Morrison, Yemin Lan, Gail L Rosen
BACKGROUND: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection--a sub-field of machine learning--can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied...
2015: BMC Bioinformatics
Francisca Araújo, Carla Pereira, Joana Costa, Cristina Barrias, Pedro L Granja, Bruno Sarmento
Although fewer in number, M-cells are considered antigen sampling cells, acting as a gateway for antigens from the gut lumen and presenting an impressive aptitude for particle transcytosis. These features make M-cells attractive targets for oral drug delivery studies, but this has been poorly explored. New and reproducible tissue-like in vitro models for studying intestinal sampling and permeability mechanisms are needed. The combination of different cell players in such models offers improved microenvironments with higher physiologic relevance...
May 2016: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Lauren L Williamson, Erin A McKenney, Zoie E Holzknecht, Christine Belliveau, John F Rawls, Susan Poulton, William Parker, Staci D Bilbo
The incidence of autoimmune and inflammatory diseases has risen dramatically in post-industrial societies. "Biome depletion" - loss of commensal microbial and multicellular organisms such as helminths (intestinal worms) that profoundly modulate the immune system - may contribute to these increases. Hyperimmune-associated disorders also affect the brain, especially neurodevelopment, and increasing evidence links early-life infection to cognitive and neurodevelopmental disorders. We have demonstrated previously that rats infected with bacteria as newborns display life-long vulnerabilities to cognitive dysfunction, a vulnerability that is specifically linked to long-term hypersensitivity of microglial cell function, the resident immune cells of the brain...
January 2016: Brain, Behavior, and Immunity
Kate D Williamson, Roger W Chapman
INTRODUCTION: Primary sclerosing cholangitis (PSC) is a progressive cholestatic disorder that ultimately can lead to cirrhosis, liver failure, malignancy and death. It is strongly associated with inflammatory bowel disease (IBD), and though a rare disease, its incidence is increasing. There are no proven medical therapies for PSC. SOURCES OF DATA: Ovid Medline was utilised to search for articles with keywords 'sclerosing cholangitis' and 'cholangiocarcinoma' and containing titles 'primary sclerosing cholangitis', and references of these papers were cross-referenced for further relevant manuscripts...
June 2015: British Medical Bulletin
Simon Roux, François Enault, Viviane Ravet, Olivier Pereira, Matthew B Sullivan
Viral metagenomics (viromics) is a tremendous tool to reveal viral taxonomic and functional diversity across ecosystems ranging from the human gut to the world's oceans. As with microbes however, there appear vast swaths of "dark matter" yet to be documented for viruses, even among relatively well-studied viral types. Here, we use viromics to explore the "Far-T4 phages" sequence space, a neighbor clade from the well-studied T4-like phages that was first detected through PCR study in seawater and subsequently identified in freshwater lakes through 454-sequenced viromes...
2015: Frontiers in Microbiology
Linh D N Nguyen, Eric Viscogliosi, Laurence Delhaes
The lung microbiome, which is believed to be stable or at least transient in healthy people, is now considered as a poly-microorganism component contributing to disease pathogenesis. Most research studies on the respiratory microbiome have focused on bacteria and their impact on lung health, but there is evidence that other non-bacterial organisms, comprising the viruses (virome) and fungi (mycobiome), are also likely to play an important role in healthy people as well as in patients. In the last few years, the lung mycobiome (previously named the fungal microbiota or microbiome) has drawn closer attention...
2015: Frontiers in Microbiology
Renata Henrique Santana, Elisa Caldeira Pires Catão, Fabyano Alvares Cardoso Lopes, Reginaldo Constantino, Cristine Chaves Barreto, Ricardo Henrique Krüger
The gut microbiota of termites allows them to thrive on a variety of different materials such as wood, litter, and soil. For that reason, they play important roles in the decomposition of biomass in diverse biomes. This function is essential in the savanna, where litter-feeding termites are one of the few invertebrates active during the dry season. In this study, we describe the gut microbiota of workers (third and fourth instars) of the species Syntermes wheeleri, a litter-feeding termite from the Brazilian savanna...
August 2015: Microbial Ecology
Phoebe Lin, Mary Bach, Mark Asquith, Aaron Y Lee, Lakshmi Akileswaran, Patrick Stauffer, Sean Davin, Yuzhen Pan, Eric D Cambronne, Martha Dorris, Justine W Debelius, Christian L Lauber, Gail Ackermann, Yoshiki V Baeza, Tejpal Gill, Rob Knight, Robert A Colbert, Joel D Taurog, Russell N Van Gelder, James T Rosenbaum
The HLA-B27 gene is a major risk factor for clinical diseases including ankylosing spondylitis, acute anterior uveitis, reactive arthritis, and psoriatic arthritis, but its mechanism of risk enhancement is not completely understood. The gut microbiome has recently been shown to influence several HLA-linked diseases. However, the role of HLA-B27 in shaping the gut microbiome has not been previously investigated. In this study, we characterize the differences in the gut microbiota mediated by the presence of the HLA-B27 gene...
2014: PloS One
Karina A Hernandez, Rachel Campbell Hooper, Tatiana Boyko, Alyssa R Golas, Michel van Harten, D Q Wu, Andrew Weinstein, C C Chu, Jason A Spector
Sutures elicit an inflammatory response, which may impede the healing process and result in wound complications. We recently reported a novel family of biocompatible, biodegradable polymers, amino acid-based poly(ester amide)s (AA-PEA), which we have shown to significantly attenuate the foreign body inflammatory response in vitro. Two types of AA-PEA (Phe-PEA and Arg-Phe-PEA) were used to coat silk or plain-gut sutures, which were implanted in the gluteus muscle of C57BL/6 mice, while the uncoated control sutures were implanted in the contralateral side...
February 2015: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
David C Dallas, Mark A Underwood, Angela M Zivkovic, J Bruce German
Premature birth rates and premature infant morbidity remain discouragingly high. Improving nourishment for these infants is the key for accelerating their development and decreasing disease risk. Dietary protein is essential for growth and development of infants. Studies on protein nourishment for premature infants have focused on protein requirements for catch-up growth, nitrogen balance, and digestive protease concentrations and activities. However, little is known about the processes and products of protein digestion in the premature infant...
April 23, 2012: Journal of Nutritional Disorders & Therapy
Valeria D'Argenio, Giorgio Casaburi, Vincenza Precone, Francesco Salvatore
Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies...
2014: BioMed Research International
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