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Microbiome

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https://www.readbyqxmd.com/read/30419949/dynamic-linear-models-guide-design-and-analysis-of-microbiota-studies-within-artificial-human-guts
#1
Justin D Silverman, Heather K Durand, Rachael J Bloom, Sayan Mukherjee, Lawrence A David
BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets. RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month...
November 12, 2018: Microbiome
https://www.readbyqxmd.com/read/30419937/association-of-bovine-major-histocompatibility-complex-bola-gene-polymorphism-with-colostrum-and-milk-microbiota-of-dairy-cows-during-the-first-week-of-lactation
#2
Hooman Derakhshani, Jan C Plaizier, Jeroen De Buck, Herman W Barkema, Ehsan Khafipour
BACKGROUND: The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation...
November 12, 2018: Microbiome
https://www.readbyqxmd.com/read/30409177/visualization-assisted-binning-of-metagenome-assemblies-reveals-potential-new-pathogenic-profiles-in-idiopathic-travelers-diarrhea
#3
Qiyun Zhu, Christopher L Dupont, Marcus B Jones, Kevin M Pham, Zhi-Dong Jiang, Herbert L DuPont, Sarah K Highlander
BACKGROUND: Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease. RESULTS: We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays...
November 8, 2018: Microbiome
https://www.readbyqxmd.com/read/30409169/cow-to-mouse-fecal-transplantations-suggest-intestinal-microbiome-as-one-cause-of-mastitis
#4
Chen Ma, Zheng Sun, Benhua Zeng, Shi Huang, Jie Zhao, Yong Zhang, Xiaoquan Su, Jian Xu, Hong Wei, Heping Zhang
BACKGROUND: Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which however are of concern in both treatment efficacy and neonate safety. Here, using bovine mastitis which is the most costly disease in the dairy industry as a model, we showed that intestinal microbiota alone can lead to mastitis. RESULTS: Fecal microbiota transplantation (FMT) from mastitis, but not healthy cows, to germ-free (GF) mice resulted in mastitis symptoms in mammary gland and inflammations in serum, spleen, and colon...
November 8, 2018: Microbiome
https://www.readbyqxmd.com/read/30396371/current-progress-and-future-opportunities-in-applications-of-bioinformatics-for-biodefense-and-pathogen-detection-report-from-the-winter-mid-atlantic-microbiome-meet-up-college-park-md-january-10-2018
#5
Jacquelyn S Meisel, Daniel J Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D Olson, Nidhi Shah, Sarah M Allard, Adam L Bazinet, Nicholas H Bergman, Alexis Brown, J Gregory Caporaso, Sean Conlan, Jocelyne DiRuggiero, Samuel P Forry, Nur A Hasan, Jason Kralj, Paul M Luethy, Donald K Milton, Brian D Ondov, Sarah Preheim, Shashikala Ratnayake, Stephanie M Rogers, M J Rosovitz, Eric G Sakowski, Nils Oliver Schliebs, Daniel D Sommer, Krista L Ternus, Gherman Uritskiy, Sean X Zhang, Mihai Pop, Todd J Treangen
The Mid-Atlantic Microbiome Meet-up (M3 ) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time...
November 5, 2018: Microbiome
https://www.readbyqxmd.com/read/30396369/an-exploration-of-prevotella-rich-microbiomes-in-hiv-and-men-who-have-sex-with-men
#6
Abigail J S Armstrong, Michael Shaffer, Nichole M Nusbacher, Christine Griesmer, Suzanne Fiorillo, Jennifer M Schneider, C Preston Neff, Sam X Li, Andrew P Fontenot, Thomas Campbell, Brent E Palmer, Catherine A Lozupone
BACKGROUND: Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-rich microbiome described in HIV-infected populations is now understood to be common in men who have sex with men (MSM) regardless of HIV status, but driving factors and potential health implications are unknown. RESULTS: Here, we further define the MSM-associated gut microbiome and describe compositional differences between the fecal microbiomes of Prevotella-rich MSM and non-MSM that may underlie observed pro-inflammatory properties...
November 5, 2018: Microbiome
https://www.readbyqxmd.com/read/30396360/the-unsolved-problem-of-otitis-media-in-indigenous-populations-a-systematic-review-of-upper-respiratory-and-middle-ear-microbiology-in-indigenous-children-with-otitis-media
#7
REVIEW
Andrea Coleman, Amanda Wood, Seweryn Bialasiewicz, Robert S Ware, Robyn L Marsh, Anders Cervin
BACKGROUND: Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic review of the literature exploring the upper airway and middle ear microbiota in relation to OM in indigenous children. METHODS: Papers targeting microbiota in relation to OM in children < 18 years indigenous to Australia, New Zealand, North America, and Greenland were sought...
November 5, 2018: Microbiome
https://www.readbyqxmd.com/read/30376898/lack-of-detection-of-a-human-placenta-microbiome-in-samples-from-preterm-and-term-deliveries
#8
Jacob S Leiby, Kevin McCormick, Scott Sherrill-Mix, Erik L Clarke, Lyanna R Kessler, Louis J Taylor, Casey E Hofstaedter, Aoife M Roche, Lisa M Mattei, Kyle Bittinger, Michal A Elovitz, Rita Leite, Samuel Parry, Frederic D Bushman
BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples...
October 30, 2018: Microbiome
https://www.readbyqxmd.com/read/30373673/a-high-throughput-sequencing-assay-to-comprehensively-detect-and-characterize-unicellular-eukaryotes-and-helminths-from-biological-and-environmental-samples
#9
Matthew V Cannon, Haikel Bogale, Lindsay Rutt, Michael Humphrys, Poonum Korpe, Priya Duggal, Jacques Ravel, David Serre
BACKGROUND: Several of the most devastating human diseases are caused by eukaryotic parasites transmitted by arthropod vectors or through food and water contamination. These pathogens only represent a fraction of all unicellular eukaryotes and helminths that are present in the environment and many uncharacterized organisms might have subtle but pervasive effects on health, including by modifying the microbiome where they reside. Unfortunately, while we have modern molecular tools to characterize bacterial and, to a lesser extent, fungal communities, we lack suitable methods to comprehensively investigate and characterize most unicellular eukaryotes and helminths: the detection of these organisms often relies on microscopy that cannot differentiate related organisms, while molecular assays can only detect the pathogens specifically tested...
October 29, 2018: Microbiome
https://www.readbyqxmd.com/read/30368244/microbial-activity-response-to-hydrogen-injection-in-thermophilic-anaerobic-digesters-revealed-by-genome-centric-metatranscriptomics
#10
Alessandra Fontana, Panagiotis G Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, Lorenzo Morelli, Irini Angelidaki, Stefano Campanaro
BACKGROUND: The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methane) or to produce high value-added compounds such as short-chain fatty acids (power-to-chemicals). Genome-centric metagenomics and metatranscriptomic analyses were performed to better understand the metabolic dynamics associated with H2 injection in two different configurations of anaerobic digesters treating acidic wastes, specifically cheese manufacturing byproducts...
October 27, 2018: Microbiome
https://www.readbyqxmd.com/read/30367675/neonatal-gut-and-respiratory-microbiota-coordinated-development-through-time-and-space
#11
Alex Grier, Andrew McDavid, Bokai Wang, Xing Qiu, James Java, Sanjukta Bandyopadhyay, Hongmei Yang, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Heidie Huyck, Ann R Falsey, David J Topham, Kristin M Scheible, Mary T Caserta, Gloria S Pryhuber, Steven R Gill
BACKGROUND: Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions and functions. Associations between microbiota at multiple sites represent an unexplored influence on the infant microbiome. Here, we examined co-occurrence patterns of gut and respiratory microbiota in pre- and full-term infants over the first year of life, a period critical to neonatal development...
October 26, 2018: Microbiome
https://www.readbyqxmd.com/read/30355348/ecologically-informed-microbial-biomarkers-and-accurate-classification-of-mixed-and-unmixed-samples-in-an-extensive-cross-study-of-human-body-sites
#12
Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues, Christian von Mering
BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers...
October 24, 2018: Microbiome
https://www.readbyqxmd.com/read/30352628/transient-o-2-pulses-direct-fe-crystallinity-and-fe-iii-reducer-gene-expression-within-a-soil-microbiome
#13
Jared Lee Wilmoth, Mary Ann Moran, Aaron Thompson
BACKGROUND: Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2 ). METHODS: We repeatedly exposed anoxic (4% H2 :96% N2 ) suspensions of soil from the Luquillo Critical Zone Observatory to 1...
October 23, 2018: Microbiome
https://www.readbyqxmd.com/read/30352623/a-diversity-generating-retroelement-encoded-by-a-globally-ubiquitous-bacteroides-phage
#14
Sean Benler, Ana Georgina Cobián-Güemes, Katelyn McNair, Shr-Hau Hung, Kyle Levi, Rob Edwards, Forest Rohwer
BACKGROUND: Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs. RESULTS: This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle...
October 23, 2018: Microbiome
https://www.readbyqxmd.com/read/30352611/species-level-bacterial-community-profiling-of-the-healthy-sinonasal-microbiome-using-pacific-biosciences-sequencing-of-full-length-16s-rrna-genes
#15
Joshua P Earl, Nithin D Adappa, Jaroslaw Krol, Archana S Bhat, Sergey Balashov, Rachel L Ehrlich, James N Palmer, Alan D Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A Cohen, Garth D Ehrlich, Joshua Chang Mell
BACKGROUND: Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy...
October 23, 2018: Microbiome
https://www.readbyqxmd.com/read/30342557/correction-to-detecting-eukaryotic-microbiota-with-single-cell-sensitivity-in-human-tissue
#16
Susanne Lager, Marcus C de Goffau, Ulla Sovio, Sharon J Peacock, Julian Parkhill, D Stephen Charnock-Jones, Gordon C S Smith
The author reported an error in an equation in the article [1].
October 20, 2018: Microbiome
https://www.readbyqxmd.com/read/30340631/the-chemodiversity-of-paddy-soil-dissolved-organic-matter-correlates-with-microbial-community-at-continental-scales
#17
Hong-Yi Li, Hang Wang, Hai-Tiao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A Gilbert, Zhi-Jian Zhang
BACKGROUND: Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition...
October 19, 2018: Microbiome
https://www.readbyqxmd.com/read/30340536/competitive-lottery-based-assembly-of-selected-clades-in-the-human-gut-microbiome
#18
Adrian J Verster, Elhanan Borenstein
BACKGROUND: While the composition of the gut microbiome has now been well described by several large-scale studies, models that can account for the range of microbiome compositions that have been observed are still lacking. One model that has been well studied in macro communities and that could be useful for understanding microbiome assembly is the competitive lottery model. This model posits that groups of organisms from a regional pool of species are able to colonize the same niche and that the first species to arrive will take over the entire niche, excluding other group members...
October 19, 2018: Microbiome
https://www.readbyqxmd.com/read/30336790/consistent-responses-of-soil-microbial-taxonomic-and-functional-attributes-to-mercury-pollution-across-china
#19
Yu-Rong Liu, Manuel Delgado-Baquerizo, Li Bi, Jun Zhu, Ji-Zheng He
BACKGROUND: The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites...
October 18, 2018: Microbiome
https://www.readbyqxmd.com/read/30336777/the-response-of-dominant-and-rare-taxa-for-fungal-diversity-within-different-root-environments-to-the-cultivation-of-bt-and-conventional-cotton-varieties
#20
Peng Li, Yong Xue, Jialiang Shi, Aihu Pan, Xueming Tang, Feng Ming
BACKGROUND: Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear. RESULTS: We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages...
October 18, 2018: Microbiome
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