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Human microbiome

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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/29242838/a-dirichlet-multinomial-bayes-classifier-for-disease-diagnosis-with-microbial-compositions
#3
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
#4
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
#5
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
#6
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
#7
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/29240761/microorganisms-in-the-human-placenta-are-associated-with-altered-cpg-methylation-of-immune-and-inflammation-related-genes
#8
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/29238751/tree-leaf-bacterial-community-structure-and-diversity-differ-along-a-gradient-of-urban-intensity
#9
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/29237568/radiomicrobiomics-advancing-along-the-gut-brain-axis-through-big-data-analysis
#10
Silvia De Santis, David Moratal, Santiago Canals
The gut-brain axis communicates the brain with the gut microbiota, a bidirectional conduit that has received increasing attention in recent years thanks to its emerging role in brain development and function. Alterations in microbiota composition have been associated to neurological and psychiatric disorders, and several studies suggest that the immune system plays a fundamental role in the gut-brain interaction. Recent advances in brain imaging and in microbiome sequencing have generated a large amount of information, yet the data from both these sources needs to be combined efficiently to extract biological meaning, and any diagnostic and/or prognostic benefit from these tools...
December 10, 2017: Neuroscience
https://www.readbyqxmd.com/read/29236996/entamoeba-species-in-south-africa-correlations-with-the-host-microbiome-parasite-burdens-and-first-description-of-entamoeba-bangladeshi-outside-of-asia
#11
Renay Ngobeni, Amidou Samie, Shannon Moonah, Koji Watanabe, William A Petri, Carol Gilchrist
Background: Diarrhea is frequent in communities without clean water, which include low-income South African populations in Giyani and Pretoria. In these populations, the amount of diarrhea caused by Entamoeba histolytica, inclusive of all ages, sexes, and human immunodeficiency virus status, is uncertain. Infection with E. histolytica can modulate the host microbiota, and a key species indicative of this is the Prevotella copri pathobiont. Methods: A cross-sectional study of patients attending gastroenterology clinics was conducted to determine the frequency and burden of 4 Entamoeba species and P...
October 8, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29233686/exercise-has-the-guts-how-physical-activity-may-positively-modulate-gut-microbiota-in-chronic-and-immune-based-diseases
#12
Roberto Codella, Livio Luzi, Ileana Terruzzi
Limited animal and human research findings suggests that exercise might have a beneficial role for health gut. Cardiorespiratory fitness has been correlates with health-associated gut parameters such as taxonomic diversity and richness. Physical exercise may augment intestinal microbial diversity through several mechanisms INCLUDING PROMOTION OF AN ANTI-INFLAMMATORY STATE. Disease-associated microbial functions WERE linked to distinct taxa in previous studies of familial type 1 diabetes mellitus (T1D). An integrated multi-approach in the study of T1D, including physical exercise, is advocated...
November 28, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/29232932/adjuvant-probiotics-and-the-intestinal-microbiome-enhancing-vaccines-and-immunotherapy-outcomes
#13
REVIEW
Luis Vitetta, Emma Tali Saltzman, Michael Thomsen, Tessa Nikov, Sean Hall
Immune defence against pathogenic agents comprises the basic premise for the administration of vaccines. Vaccinations have hence prevented millions of infectious illnesses, hospitalizations and mortality. Acquired immunity comprises antibody and cell mediated responses and is characterized by its specificity and memory. Along a similar congruent yet diverse mode of disease prevention, the human host has negotiated from in utero and at birth with the intestinal commensal bacterial cohort to maintain local homeostasis in order to achieve immunological tolerance in the new born...
December 11, 2017: Vaccines
https://www.readbyqxmd.com/read/29230218/endogenous-antimicrobial-peptide-expression-in-response-to-bacterial-epidermal-colonization
#14
REVIEW
Michael Brandwein, Zvi Bentwich, Doron Steinberg
Bacterial commensal colonization of human skin is vital for the training and maintenance of the skin's innate and adaptive immune functions. In addition to its physical barrier against pathogen colonization, the skin expresses a variety of antimicrobial peptides (AMPs) which are expressed constitutively and induced in response to pathogenic microbial stimuli. These AMPs are differentially effective against a suite of microbial skin colonizers, including both bacterial and fungal residents of the skin. We review the breadth of microorganism-induced cutaneous AMP expression studies and their complementary findings on the efficacy of skin AMPs against different bacterial and fungal species...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29230215/potential-effects-of-horizontal-gene-exchange-in-the-human-gut
#15
Aaron Lerner, Torsten Matthias, Rustam Aminov
Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host-microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29228991/the-rumen-microbiome-as-a-reservoir-of-antimicrobial-resistance-and-pathogenicity-genes-is-directly-affected-by-diet-in-beef-cattle
#16
Marc D Auffret, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke, R John Wallace, Tom C Freeman, Robert Stewart, Mick Watson, Rainer Roehe
BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate...
December 11, 2017: Microbiome
https://www.readbyqxmd.com/read/29228609/bacteriome-and-mycobiome-associations-in-oral-tongue-cancer
#17
Pranab K Mukherjee, Hannah Wang, Mauricio Retuerto, Huan Zhang, Brian Burkey, Mahmoud A Ghannoum, Charis Eng
Squamous cell carcinoma of the oral (mobile) tongue (OMTC), a non-human papilloma virus-associated oral cancer, is rapidly increasing without clear etiology. Poor oral hygiene has been associated with oral cancers, suggesting that oral bacteriome (bacterial community) and mycobiome (fungal community) could play a role. While the bacteriome is increasingly recognized as an active participant in health, the role of the mycobiome has not been studied in OMTC. Tissue DNA was extracted from 39 paired tumor and adjacent normal tissues from patients with OMTC...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228398/organophosphorus-compounds-at-80-some-old-and-new-issues
#18
Lucio G Costa
One of the major classes of pesticides is that of the organophosphates (OPs). Initial developments date back almost two centuries but it was only in the mid-1940s that OPs reached a prominent status as insecticides, a status that, albeit declining, is still ongoing. OPs are highly toxic to non-target species including humans, the primary effects being an acute cholinergic toxicity (responsible for thousands of poisoning each year) and a delayed polyneuropathy. Several issues of current debate and investigation on the toxicology of OPs are discussed in this brief review...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29228222/human-microbiomes-influence-cancer-therapy
#19
Charlie Schmidt
No abstract text is available yet for this article.
December 8, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29227922/evolution-of-virulence-in-enterococcus-faecium-a-hospital-adapted-opportunistic-pathogen
#20
REVIEW
Wei Gao, Benjamin P Howden, Timothy P Stinear
Enterococci are long-standing members of the human microbiome and they are also widely distributed in nature. However, with the surge of antibiotic-resistance in recent decades, two enterococcal species (Enterococcus faecalis and Enterococcus faecium) have emerged to become significant nosocomial pathogens, acquiring extensive antibiotic resistance. In this review, we summarize what is known about the evolution of virulence in E. faecium, highlighting a specific clone of E. faecium called ST796 that has emerged recently and spread globally...
December 8, 2017: Current Opinion in Microbiology
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