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Microbiome

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https://www.readbyqxmd.com/read/28915923/season-but-not-symbiont-state-drives-microbiome-structure-in-the-temperate-coral-astrangia-poculata
#1
Koty H Sharp, Zoe A Pratte, Allison H Kerwin, Randi D Rotjan, Frank J Stewart
BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#2
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28911333/profiling-bacterial-communities-by-minion-sequencing-of-ribosomal-operons
#3
Lee J Kerkhof, Kevin P Dillon, Max M Häggblom, Lora R McGuinness
BACKGROUND: An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28903767/treatment-of-biofilms-in-bacterial-vaginosis-by-an-amphoteric-tenside-pessary-clinical-study-and-microbiota-analysis
#4
Cornelia Gottschick, Zhi-Luo Deng, Marius Vital, Clarissa Masur, Christoph Abels, Dietmar H Pieper, Manfred Rohde, Werner Mendling, Irene Wagner-Döbler
BACKGROUND: Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like preterm labor. BV is characterized by a high recurrence rate for which biofilms frequently found on vaginal epithelial cells may be a reason. RESULTS: Here, we report a controlled randomized clinical trial that tested the safety and effectiveness of a newly developed pessary containing an amphoteric tenside (WO3191) to disrupt biofilms after metronidazole treatment of BV...
September 13, 2017: Microbiome
https://www.readbyqxmd.com/read/28893308/more-than-2500%C3%A2-years-of-oil-exposure-shape-sediment-microbiomes-with-the-potential-for-syntrophic-degradation-of-hydrocarbons-linked-to-methanogenesis
#5
Antonios Michas, Gisle Vestergaard, Kathleen Trautwein, Pavlos Avramidis, Dimitris G Hatzinikolaou, Constantinos E Vorgias, Heinz Wilkes, Ralf Rabus, Michael Schloter, Anne Schöler
BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods...
September 11, 2017: Microbiome
https://www.readbyqxmd.com/read/28877764/perilipin-2-modulates-dietary-fat-induced-microbial-global-gene-expression-profiles-in-the-mouse-intestine
#6
Xuejian Xiong, Elise S Bales, Diana Ir, Charles E Robertson, James L McManaman, Daniel N Frank, John Parkinson
BACKGROUND: Intestinal microbiota are critical determinants of obesity and metabolic disease risk. In previous work, we showed that deletion of the cytoplasmic lipid droplet (CLD) protein perilipin-2 (Plin2) modulates gut microbial community structure and abrogates long-term deleterious effects of a high-fat (HF) diet in mice. However, the impact of Plin2 on microbiome function is unknown. RESULTS: Here, we used metatranscriptomics to identify differences in microbiome transcript expression in WT and Plin2-null mice following acute exposure to high-fat/low-carbohydrate (HF) or low-fat/high-carbohydrate (LF) diets...
September 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28870257/enrichment-of-beneficial-bacteria-in-the-skin-microbiota-of-bats-persisting-with-white-nose-syndrome
#7
Virginie Lemieux-Labonté, Anouk Simard, Craig K R Willis, François-Joseph Lapointe
BACKGROUND: Infectious diseases of wildlife are increasing worldwide with implications for conservation and human public health. The microbiota (i.e. microbial community living on or in a host) could influence wildlife disease resistance or tolerance. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), has killed millions of hibernating North American bats since 2007. We characterized the skin microbiota of naïve, pre-WNS little brown bats (Myotis lucifugus) from three WNS-negative hibernation sites and persisting, previously exposed bats from three WNS-positive sites to test the hypothesis that the skin microbiota of bats shifts following WNS invasion...
September 5, 2017: Microbiome
https://www.readbyqxmd.com/read/28870234/collection-of-non-meconium-stool-on-fecal-occult-blood-cards-is-an-effective-method-for-fecal-microbiota-studies-in-infants
#8
Wendy S W Wong, Nicole Clemency, Elisabeth Klein, Marina Provenzano, Ramaswamy Iyer, John E Niederhuber, Suchitra K Hourigan
BACKGROUND: Effective methods are needed to collect fecal samples from children for large-scale microbiota studies. Stool collected on fecal occult blood test (FOBT) cards that can be mailed provides an effective solution; however, the quality of sequencing resulting from this method is unknown. The aim of this study is to compare microbiota metrics of 16S ribosomal RNA (rRNA) gene sequencing from stool and meconium collected on FOBT cards with stool collected in an Eppendorf tube (ET) under different conditions...
September 5, 2017: Microbiome
https://www.readbyqxmd.com/read/28870230/pre-pregnancy-weight-gestational-weight-gain-and-the-gut-microbiota-of-mothers-and-their-infants
#9
Maggie A Stanislawski, Dana Dabelea, Brandie D Wagner, Marci K Sontag, Catherine A Lozupone, Merete Eggesbø
BACKGROUND: Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at the time of delivery and their infants in early life. In this study, we performed 16S rRNA gene sequencing on gut microbiota samples from 169 women 4 days after delivery and from the 844 samples of their infants at six timepoints during the first 2 years of life...
September 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28865481/members-of-the-candidate-phyla-radiation-are-functionally-differentiated-by-carbon-and-nitrogen-cycling-capabilities
#10
R E Danczak, M D Johnston, C Kenah, M Slattery, K C Wrighton, M J Wilkins
BACKGROUND: The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution...
September 2, 2017: Microbiome
https://www.readbyqxmd.com/read/28863784/erratum-to-whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#11
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
No abstract text is available yet for this article.
September 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28859671/the-structure-of-the-brassica-napus-seed-microbiome-is-cultivar-dependent-and-affects-the-interactions-of-symbionts-and-pathogens
#12
Daria Rybakova, Riccardo Mancinelli, Mariann Wikström, Ann-Sofie Birch-Jensen, Joeke Postma, Ralf-Udo Ehlers, Simon Goertz, Gabriele Berg
BACKGROUND: Although the plant microbiome is crucial for plant health, little is known about the significance of the seed microbiome. Here, we studied indigenous bacterial communities associated with the seeds in different cultivars of oilseed rape and their interactions with symbiotic and pathogenic microorganisms. RESULTS: We found a high bacterial diversity expressed by tight bacterial co-occurrence networks within the rape seed microbiome, as identified by llumina MiSeq amplicon sequencing...
September 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28859695/learning-microbial-community-structures-with-supervised-and-unsupervised-non-negative-matrix-factorization
#13
Yun Cai, Hong Gu, Toby Kenney
BACKGROUND: Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data...
August 31, 2017: Microbiome
https://www.readbyqxmd.com/read/28841911/blood-as-a-route-of-transmission-of-uterine-pathogens-from-the-gut-to-the-uterus-in-cows
#14
Soo Jin Jeon, Federico Cunha, Achilles Vieira-Neto, Rodrigo C Bicalho, Svetlana Lima, Marcela L Bicalho, Klibs N Galvão
BACKGROUND: Metritis is an inflammatory disease of the uterus caused by bacterial infection, particularly Bacteroides, Porphyromonas, and Fusobacterium. Bacteria from the environment, feces, or vagina are believed to be the only sources of uterine contamination. Blood seeps into the uterus after calving; therefore, we hypothesized that blood could also be a seeding source of uterine bacteria. Herein, we compared bacterial communities from blood, feces, and uterine samples from the same cows at 0 and 2 days postpartum using deep sequencing and qPCR...
August 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28841836/oxalobacter-formigenes-associated-host-features-and-microbial-community-structures-examined-using-the-american-gut-project
#15
Menghan Liu, Hyunwook Koh, Zachary D Kurtz, Thomas Battaglia, Amanda PeBenito, Huilin Li, Lama Nazzal, Martin J Blaser
BACKGROUND: Increasing evidence shows the importance of the commensal microbe Oxalobacter formigenes in regulating host oxalate homeostasis, with effects against calcium oxalate kidney stone formation, and other oxalate-associated pathological conditions. However, limited understanding of O. formigenes in humans poses difficulties for designing targeted experiments to assess its definitive effects and sustainable interventions in clinical settings. We exploited the large-scale dataset from the American Gut Project (AGP) to study O...
August 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28838324/microbial-regulation-of-microrna-expression-in-the-amygdala-and-prefrontal-cortex
#16
Alan E Hoban, Roman M Stilling, Gerard M Moloney, Rachel D Moloney, Fergus Shanahan, Timothy G Dinan, John F Cryan, Gerard Clarke
BACKGROUND: There is growing evidence for a role of the gut microbiome in shaping behaviour relevant to many psychiatric and neurological disorders. Preclinical studies using germ-free (GF) animals have been essential in contributing to our current understanding of the potential importance of the host microbiome for neurodevelopment and behaviour. In particular, it has been repeatedly demonstrated that manipulation of the gut microbiome modulates anxiety-like behaviours. The neural circuits that underlie anxiety- and fear-related behaviours are complex and heavily depend on functional communication between the amygdala and prefrontal cortex (PFC)...
August 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28837002/early-gut-mycobiota-and-mother-offspring-transfer
#17
Kasper Schei, Ekaterina Avershina, Torbjørn Øien, Knut Rudi, Turid Follestad, Saideh Salamati, Rønnaug Astri Ødegård
BACKGROUND: The fungi in the gastrointestinal tract, the gut mycobiota, are now recognised as a significant part of the gut microbiota, and they may be important to human health. In contrast to the adult gut mycobiota, the establishment of the early gut mycobiota has never been described, and there is little knowledge about the fungal transfer from mother to offspring. METHODS: In a prospective cohort, we followed 298 pairs of healthy mothers and offspring from 36 weeks of gestation until 2 years of age (1516 samples) and explored the gut mycobiota in maternal and offspring samples...
August 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28835260/genomic-insights-into-potential-interdependencies-in-microbial-hydrocarbon-and-nutrient-cycling-in-hydrothermal-sediments
#18
Nina Dombrowski, Kiley W Seitz, Andreas P Teske, Brett J Baker
BACKGROUND: Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data...
August 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28821301/space-type-radiation-induces-multimodal-responses-in-the-mouse-gut-microbiome-and-metabolome
#19
David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory Nelson, Martin Hauer-Jensen, Marjan Boerma, Jonathan Braun, Amrita K Cheema
BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel...
August 18, 2017: Microbiome
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#20
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
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