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Microbiome

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https://www.readbyqxmd.com/read/28335814/symbiosis-and-microbiome-flexibility-in-calcifying-benthic-foraminifera-of-the-great-barrier-reef
#1
Martina Prazeres, Tracy Ainsworth, T Edward Roberts, John M Pandolfi, William Leggat
BACKGROUND: Symbiosis is a phenomenon that allows organisms to colonise a wide range of environments and occupy a variety of ecological niches in marine environments. Large benthic foraminifera (LBF) are crucial marine calcifiers that rely on photo-endosymbionts for growth and calcification, yet the influence of environmental conditions in shaping their interactions with prokaryotic and eukaryotic associates is poorly known. RESULTS: Here, we used next-generation sequencing to identify eukaryotic photosynthesizing and prokaryotic microbes associated with the common LBF Amphistegina lobifera across a physio-chemical gradient on the Great Barrier Reef (GBR)...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#2
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28330508/proteobacteria-explain-significant-functional-variability-in-the-human-gut-microbiome
#3
Patrick H Bradley, Katherine S Pollard
BACKGROUND: While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals. RESULTS: To account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28320468/subgingival-microbiota-dysbiosis-in-systemic-lupus-erythematosus-association-with-periodontal-status
#4
Jôice Dias Corrêa, Débora Cerqueira Calderaro, Gilda Aparecida Ferreira, Santuza Maria Souza Mendonça, Gabriel R Fernandes, E Xiao, Antônio Lúcio Teixeira, Eugene J Leys, Dana T Graves, Tarcília Aparecida Silva
BACKGROUND: Periodontitis results from the interaction between a subgingival biofilm and host immune response. Changes in biofilm composition are thought to disrupt homeostasis between the host and subgingival bacteria resulting in periodontal damage. Chronic systemic inflammatory disorders have been shown to affect the subgingival microbiota and clinical periodontal status. However, this relationship has not been examined in subjects with systemic lupus erythematosus (SLE). The objective of our study was to investigate the influence of SLE on the subgingival microbiota and its connection with periodontal disease and SLE activity...
March 20, 2017: Microbiome
https://www.readbyqxmd.com/read/28320465/reduced-microbial-diversity-in-adult-survivors-of-childhood-acute-lymphoblastic-leukemia-and-microbial-associations-with-increased-immune-activation
#5
Ling Ling Chua, Reena Rajasuriar, Mohamad Shafiq Azanan, Noor Kamila Abdullah, Mei San Tang, Soo Ching Lee, Yin Ling Woo, Yvonne Ai Lian Lim, Hany Ariffin, P'ng Loke
BACKGROUND: Adult survivors of childhood cancers such as acute lymphoblastic leukemia (ALL) have health problems that persist or develop years after cessation of therapy. These late effects include chronic inflammation-related comorbidities such as obesity and type 2 diabetes, but the underlying cause is poorly understood. RESULTS: We compared the anal microbiota composition of adult survivors of childhood ALL (N = 73) with healthy control subjects (N = 61)...
March 20, 2017: Microbiome
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#6
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28285599/microbiome-and-metabolome-modifying-effects-of-several-cardiovascular-disease-interventions-in-apo-e-mice
#7
Paul M Ryan, Lis E E London, Trent C Bjorndahl, Rupasri Mandal, Kiera Murphy, Gerald F Fitzgerald, Fergus Shanahan, R Paul Ross, David S Wishart, Noel M Caplice, Catherine Stanton
BACKGROUND: There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT)...
March 13, 2017: Microbiome
https://www.readbyqxmd.com/read/28283029/legal-immigrants-invasion-of-alien-microbial-communities-during-winter-occurring-desert-dust-storms
#8
Tobias Weil, Carlotta De Filippo, Davide Albanese, Claudio Donati, Massimo Pindo, Lorenzo Pavarini, Federico Carotenuto, Massimiliano Pasqui, Luisa Poto, Jacopo Gabrieli, Carlo Barbante, Birgit Sattler, Duccio Cavalieri, Franco Miglietta
BACKGROUND: A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust...
March 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28274256/intestinal-dysbiosis-in-preterm-infants-preceding-necrotizing-enterocolitis-a-systematic-review-and-meta-analysis
#9
REVIEW
Mohan Pammi, Julia Cope, Phillip I Tarr, Barbara B Warner, Ardythe L Morrow, Volker Mai, Katherine E Gregory, J Simon Kroll, Valerie McMurtry, Michael J Ferris, Lars Engstrand, Helene Engstrand Lilja, Emily B Hollister, James Versalovic, Josef Neu
BACKGROUND: Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results. METHODS AND RESULTS: Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies...
March 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28264712/erratum-to-the-gut-microbiota-in-conventional-and-serrated-precursors-of-colorectal-cancer
#10
Brandilyn A Peters, Christine Dominianni, Jean A Shapiro, Timothy R Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B Hayes, Jiyoung Ahn
No abstract text is available yet for this article.
March 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28253936/simple-discovery-of-bacterial-biocatalysts-from-environmental-samples-through-functional-metaproteomics
#11
Premankur Sukul, Sina Schäkermann, Julia E Bandow, Anna Kusnezowa, Minou Nowrousian, Lars I Leichert
Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information and our capacity of functionally screening for desired activities. Here, we present a simple workflow that combines functional metaproteomics and metagenomics, which facilitates the unmediated and direct discovery of biocatalysts in environmental samples. To identify the entirety of lipolytic biocatalysts in a soil sample contaminated with used cooking oil, we detected all proteins active against a fluorogenic substrate in sample's metaproteome using a 2D-gel zymogram...
March 3, 2017: Microbiome
https://www.readbyqxmd.com/read/28253911/childhood-bmi-in-relation-to-microbiota-in-infancy-and-lifetime-antibiotic-use
#12
K Korpela, M A C Zijlmans, M Kuitunen, K Kukkonen, E Savilahti, A Salonen, C de Weerth, W M de Vos
BACKGROUND: Children with high body mass index (BMI) at preschool age are at risk of developing obesity. Early identification of factors that increase the risk of excessive weight gain could help direct preventive actions. The intestinal microbiota and antibiotic use have been identified as potential modulators of early metabolic programming and weight development. To test if the early microbiota composition is associated with later BMI, and if antibiotic use modifies this association, we analysed the faecal microbiota composition at 3 months and the BMI at 5-6 years in two cohorts of healthy children born vaginally at term in the Netherlands (N = 87) and Finland (N = 75)...
March 3, 2017: Microbiome
https://www.readbyqxmd.com/read/28253908/normalization-and-microbial-differential-abundance-strategies-depend-upon-data-characteristics
#13
Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R Hyde, Rob Knight
BACKGROUND: Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge...
March 3, 2017: Microbiome
https://www.readbyqxmd.com/read/28231859/structural-variability-and-niche-differentiation-in-the-rhizosphere-and-endosphere-bacterial-microbiome-of-field-grown-poplar-trees
#14
Bram Beckers, Michiel Op De Beeck, Nele Weyens, Wout Boerjan, Jaco Vangronsveld
BACKGROUND: The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive...
February 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28222761/new-evidences-on-the-altered-gut-microbiota-in-autism-spectrum-disorders
#15
Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Daniela Renzi, Antonio Calabrò, Carlotta De Filippo
BACKGROUND: Autism spectrum disorders (ASDs) are neurodevelopmental conditions characterized by social and behavioural impairments. In addition to neurological symptoms, ASD subjects frequently suffer from gastrointestinal abnormalities, thus implying a role of the gut microbiota in ASD gastrointestinal pathophysiology. RESULTS: Here, we characterized the bacterial and fungal gut microbiota in a cohort of autistic individuals demonstrating the presence of an altered microbial community structure...
February 22, 2017: Microbiome
https://www.readbyqxmd.com/read/28212659/erratum-to-ancient-bacteria-of-the-%C3%A3-tzi-s-microbiome-a-genomic-tale-from-the-copper-age
#16
Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
No abstract text is available yet for this article.
February 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#17
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28196541/erratum-to-evolution-of-gut-microbiota-composition-from-birth-to-24%C3%A2-weeks-in-the-infantmet-cohort
#18
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R Paul Ross, C Anthony Ryan, Paul W O'Toole, Catherine Stanton
No abstract text is available yet for this article.
February 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28187782/sputum-dna-sequencing-in-cystic-fibrosis-non-invasive-access-to-the-lung-microbiome-and-to-pathogen-details
#19
Rounak Feigelman, Christian R Kahlert, Florent Baty, Frank Rassouli, Rebekka L Kleiner, Philipp Kohler, Martin H Brutsche, Christian von Mering
BACKGROUND: Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution...
February 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28179023/optimization-of-dna-extraction-for-advancing-coral-microbiota-investigations
#20
Laura Weber, Emelia DeForce, Amy Apprill
BACKGROUND: DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition...
February 8, 2017: Microbiome
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