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https://www.readbyqxmd.com/read/29245010/our-gut-microbiome-the-evolving-inner-self
#1
REVIEW
Parag Kundu, Eran Blacher, Eran Elinav, Sven Pettersson
The "holobiont" concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality...
December 14, 2017: Cell
https://www.readbyqxmd.com/read/29244764/the-seagrass-holobiont-and-its-microbiome
#2
REVIEW
Kelly Ugarelli, Seemanti Chakrabarti, Peeter Laas, Ulrich Stingl
Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses...
December 15, 2017: Microorganisms
https://www.readbyqxmd.com/read/29244059/the-mediterranean-diet-metabolic-and-molecular-mechanisms
#3
Valeria Tosti, Beatrice Bertozzi, Luigi Fontana
Consuming a Mediterranean diet rich in minimally processed plant foods has been associated with a reduced risk of developing multiple chronic diseases and increased life expectancy. Data from several randomized clinic trials have demonstrated a beneficial effect in the primary and secondary prevention of cardiovascular disease, type 2 diabetes, atrial fibrillation and breast cancer. The exact mechanism by which an increased adherence to the traditional Mediterranean diet exerts its favorable effects is not known...
December 13, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29243124/gut-microbiome-a-new-player-in-gastrointestinal-disease
#4
Gregor Gorkiewicz, Alexander Moschen
The gastrointestinal (GI) tract harbors a diverse and host-specific gut microbial community. Whereas host-microbe interactions are based on homeostasis and mutualism, the microbiome also contributes to disease development. In this review, we summarize recent findings connecting the GI microbiome with GI disease. Starting with a description of biochemical factors shaping microbial compositions in each gut segment along the longitudinal axis, improved histological techniques enabling high resolution visualization of the spatial microbiome structure are highlighted...
December 14, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29242838/a-dirichlet-multinomial-bayes-classifier-for-disease-diagnosis-with-microbial-compositions
#5
Xiang Gao, Huaiying Lin, Qunfeng Dong
Dysbiosis of microbial communities is associated with various human diseases, raising the possibility of using microbial compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling microbial compositions with Dirichlet-multinomial distributions, which are widely used to model multicategorical count data with extra variation. The parameters of the Dirichlet-multinomial distributions are estimated from training microbiome data sets based on maximum likelihood. The posterior probability of a microbiome sample belonging to a disease or healthy category is calculated based on Bayes' theorem, using the likelihood values computed from the estimated Dirichlet-multinomial distribution, as well as a prior probability estimated from the training microbiome data set or previously published information on disease prevalence...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242834/novel-its1-fungal-primers-for-characterization-of-the-mycobiome
#6
Mykhaylo Usyk, Christine P Zolnik, Hitesh Patel, Michael H Levi, Robert D Burk
Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242832/persistence-of-supplemented-bifidobacterium-longum-subsp-infantis-evc001-in-breastfed-infants
#7
Steven A Frese, Andra A Hutton, Lindsey N Contreras, Claire A Shaw, Michelle C Palumbo, Giorgio Casaburi, Gege Xu, Jasmine C C Davis, Carlito B Lebrilla, Bethany M Henrick, Samara L Freeman, Daniela Barile, J Bruce German, David A Mills, Jennifer T Smilowitz, Mark A Underwood
Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32)...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242367/subspecies-in-the-global-human-gut-microbiome
#8
Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta-Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies)...
December 14, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29241587/associations-between-infant-fungal-and-bacterial-dysbiosis-and-childhood-atopic-wheeze-in-a-nonindustrialized-setting
#9
Marie-Claire Arrieta, Andrea Arévalo, Leah Stiemsma, Pedro Dimitriu, Martha E Chico, Sofia Loor, Maritza Vaca, Rozlyn C T Boutin, Evan Morien, Mingliang Jin, Stuart E Turvey, Jens Walter, Laura Wegener Parfrey, Philip J Cooper, Brett Finlay
BACKGROUND: Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. OBJECTIVE: We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting...
November 30, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29241453/bile-acid-is-a-significant-host-factor-shaping-the-gut-microbiome-of-diet-induced-obese-mice
#10
Xiaojiao Zheng, Fengjie Huang, Aihua Zhao, Sha Lei, Yunjing Zhang, Guoxiang Xie, Tianlu Chen, Chun Qu, Cynthia Rajani, Bing Dong, Defa Li, Wei Jia
BACKGROUND: Intestinal bacteria are known to regulate bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulation of the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regulate the gut microbiota with their strong antimicrobial activities. It remains unclear, however, how mammalian BAs cross-talk with gut microbiome and shape microbial composition in a dynamic and interactive way. RESULTS: We quantitatively profiled small molecule metabolites derived from host-microbial co-metabolism in mice, demonstrating that BAs were the most significant factor correlated with microbial alterations among all types of endogenous metabolites...
December 14, 2017: BMC Biology
https://www.readbyqxmd.com/read/29241213/antibiotics-induced-obesity-a-mitochondrial-perspective
#11
Melisa J Andrade, Chinchu Jayaprakash, Smitha Bhat, Nikolaos Evangelatos, Angela Brand, Kapaettu Satyamoorthy
Antibiotics are the first line of treatment against infections and have contributed immensely to reduce the morbidity and mortality rates. Recently, extensive use of antibiotics has led to alterations of the gut microbiome, predisposition to various diseases and most importantly, increase in the emergence of antibiotic-resistant bacteria, which poses a major threat to global public health. Another major issue faced worldwide due to unregulated use of antibiotics in children as well as in adults is the influence of metabolism and body weight homeostasis, leading to obesity...
December 15, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/29241038/through-the-scope-darkly-the-gut-mycobiome-comes-into-focus
#12
Nydiaris Hernández-Santos, Bruce S Klein
The gut microbiome is comprised of microbes from multiple kingdoms, including bacteria, but also fungi, viruses, and perhaps other agents. In this issue of Cell Host & Microbe, Jiang et al. (2017) reveal that fungal monocolonization after antibiotic-mediated depletion of intestinal bacteria prevents colitis and influenza, thus highlighting beneficial roles of fungi.
December 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29240834/discovery-of-carbamate-degrading-enzymes-by-functional-metagenomics
#13
Lisa Ufarté, Elisabeth Laville, Sophie Duquesne, Diego Morgavi, Patrick Robe, Christophe Klopp, Angeline Rizzo, Sandra Pizzut-Serin, Gabrielle Potocki-Veronese
Bioremediation of pollutants is a major concern worldwide, leading to the research of new processes to break down and recycle xenobiotics and environment contaminating polymers. Among them, carbamates have a very broad spectrum of uses, such as toxinogenic pesticides or elastomers. In this study, we mined the bovine rumen microbiome for carbamate degrading enzymes. We isolated 26 hit clones exhibiting esterase activity, and were able to degrade at least one of the targeted polyurethane and pesticide carbamate compounds...
2017: PloS One
https://www.readbyqxmd.com/read/29240761/microorganisms-in-the-human-placenta-are-associated-with-altered-cpg-methylation-of-immune-and-inflammation-related-genes
#14
Martha Scott Tomlinson, Paige A Bommarito, Elizabeth M Martin, Lisa Smeester, Raina N Fichorova, Andrew B Onderdonk, Karl C K Kuban, T Michael O'Shea, Rebecca C Fry
Microorganisms in the placenta have been linked to adverse pregnancy outcomes as well as neonatal illness. Inflammation in the placenta has been identified as a contributing factor in this association, but the underlying biological mechanisms are not yet fully understood. The placental epigenome may serve as an intermediate between placental microbes and inflammation, contributing to adverse outcomes in the offspring. In the present study, genome-wide DNA methylation (n = 486,428 CpG sites) of 84 placentas was analyzed in relation to 16 species of placental microorganisms using samples collected from the Extremely Low Gestation Age Newborns (ELGAN) cohort...
2017: PloS One
https://www.readbyqxmd.com/read/29240375/an-integrative-review-of-current-research-on-the-role-of-the-female-urinary-microbiota-in-overactive-bladder-symptoms
#15
Kimberly J Angelini
This integrative review explores current evidence on microbiota of the female urinary tract as it relates to overactive bladder (OAB) symptoms. Six articles were identified for review. Findings suggest a possible link between the female urinary microbiome and OAB symptom presentation.
March 2017: Urologic Nursing
https://www.readbyqxmd.com/read/29240224/metabolic-characterization-of-anaerobic-fungi-provides-a-path-forward-for-bioprocessing-of-crude-lignocellulose
#16
John K Henske, St Elmo Wilken, Kevin V Solomon, Chuck R Smallwood, Vaithiyalingam Shutthanandan, James E Evans, Michael K Theodorou, Michelle A O'Malley
The conversion of lignocellulose-rich biomass to bio-based chemicals and higher order fuels remains a grand challenge, as single-microbe approaches often cannot drive both deconstruction and chemical production steps. In contrast, consortia based bioprocessing leverages the strengths of different microbes to distribute metabolic loads and achieve process synergy, product diversity, and bolster yields. Here, we describe a biphasic fermentation scheme that combines the lignocellulolytic action of anaerobic fungi isolated from large herbivores with domesticated microbes for bioproduction...
December 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29238751/tree-leaf-bacterial-community-structure-and-diversity-differ-along-a-gradient-of-urban-intensity
#17
Isabelle Laforest-Lapointe, Christian Messier, Steven W Kembel
Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome...
November 2017: MSystems
https://www.readbyqxmd.com/read/29238353/rhizosphere-microbiome-recruited-from-a-suppressive-compost-improves-plant-fitness-and-increases-protection-against-vascular-wilt-pathogens-of-tomato
#18
Anastasis Antoniou, Maria-Dimitra Tsolakidou, Ioannis A Stringlis, Iakovos S Pantelides
Suppressive composts represent a sustainable approach to combat soilborne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts are often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost's microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29238339/comparing-the-healthy-nose-and-nasopharynx-microbiota-reveals-continuity-as-well-as-niche-specificity
#19
Ilke De Boeck, Stijn Wittouck, Sander Wuyts, Eline F M Oerlemans, Marianne F L van den Broek, Dieter Vandenheuvel, Olivier Vanderveken, Sarah Lebeer
To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collected paired nasal and nasopharyngeal swabs from 100 healthy participants in a citizen-science project. High-throughput 16S rRNA gene V4 amplicon sequencing was performed and samples were processed using the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29238198/oral-microbiome-and-peri-implant-diseases-where-are-we-now
#20
REVIEW
Rafał Pokrowiecki, Agnieszka Mielczarek, Tomasz Zaręba, Stefan Tyski
Peri-implant infective diseases (PIIDs) in oral implantology are commonly known as peri-implant mucositis (PIM) and periimplantitis (PI). While PIM is restricted to the peri-implant mucosa and is reversible, PI also affects implant-supporting bone and, therefore, is very difficult to eradicate. PIIDs in clinical outcome may resemble gingivitis and periodontitis, as they share similar risk factors. However, recent study in the field of proteomics and other molecular studies indicate that PIIDs exhibit significant differences when compared to periodontal diseases...
2017: Therapeutics and Clinical Risk Management
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