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https://www.readbyqxmd.com/read/30003144/the-current-and-future-state-of-department-of-defense-dod-microbiome-research-a-summary-of-the-inaugural-dod-tri-service-microbiome-consortium-informational-meeting
#1
Sarah Glaven, Kenneth Racicot, Dagmar H Leary, J Philip Karl, Steven Arcidiacono, Blair C R Dancy, Linda A Chrisey, Jason W Soares
The Tri-Service Microbiome Consortium (TSMC) was recently established to enhance collaboration, coordination, and communication of microbiome research among Department of Defense (DoD) organizations. The TSMC aims to serve as a forum for sharing information related to DoD microbiome research, policy, and applications, to monitor global advances relevant to human health and performance, to identify priority objectives, and to facilitate Tri-Service (Army, Navy, and Air Force) collaborative research. The inaugural TSMC workshop held on 10 to 11 May 2017 brought together almost 100 attendees from across the DoD and several key DoD partners...
July 2018: MSystems
https://www.readbyqxmd.com/read/30003143/critical-assessment-of-metagenome-interpretation-enters-the-second-round
#2
EDITORIAL
Andreas Bremges, Alice C McHardy
No abstract text is available yet for this article.
July 2018: MSystems
https://www.readbyqxmd.com/read/30003142/erratum-for-grieneisen-and-blekhman-crowdsourcing-our-national-gut
#3
Laura E Grieneisen, Ran Blekhman
[This corrects the article DOI: 10.1128/mSystems.00060-18.].
July 2018: MSystems
https://www.readbyqxmd.com/read/29984314/microbial-community-cohesion-mediates-community-turnover-in-unperturbed-aquifers
#4
Robert E Danczak, Michael D Johnston, Chris Kenah, Michael Slattery, Michael J Wilkins
Microbial ecological processes are frequently studied in the presence of perturbations rather than in undisturbed environments, despite the relatively stable conditions dominating many microbial habitats. To examine processes influencing microbial community structuring in the absence of strong external perturbations, three unperturbed aquifers in Ohio (Greene, Licking, and Athens) were sampled over 2 years and analyzed using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Redox conditions ranging from highly reducing to more oxidizing distinguished aquifer geochemistry across the three locations...
July 2018: MSystems
https://www.readbyqxmd.com/read/29963641/characterization-of-wild-and-captive-baboon-gut-microbiota-and-their-antibiotic-resistomes
#5
Pablo Tsukayama, Manish Boolchandani, Sanket Patel, Erica C Pehrsson, Molly K Gibson, Kenneth L Chiou, Clifford J Jolly, Jeffrey Rogers, Jane E Phillips-Conroy, Gautam Dantas
Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes...
May 2018: MSystems
https://www.readbyqxmd.com/read/29963640/identification-of-pathogenicity-associated-loci-in-klebsiella-pneumoniae-from-hospitalized-patients
#6
Rebekah M Martin, Jie Cao, Weisheng Wu, Lili Zhao, David M Manthei, Ali Pirani, Evan Snitkin, Preeti N Malani, Krishna Rao, Michael A Bachman
Despite insights gained through experimental models, the set of bacterial genes important for human infection is unclear for many of our most threatening pathogens. Klebsiella pneumoniae is a leading cause of health care-associated infections (HAIs) and commonly colonizes hospitalized patients, but the factors that determine whether a particular isolate causes disease or remains a colonizer are poorly understood. To identify bacterial genes associated with K. pneumoniae infection, a case-control study was performed comparing infected and asymptomatic colonized patients...
May 2018: MSystems
https://www.readbyqxmd.com/read/29963639/asymptomatic-intestinal-colonization-with-protist-blastocystis-is-strongly-associated-with-distinct-microbiome-ecological-patterns
#7
M E Nieves-Ramírez, O Partida-Rodríguez, I Laforest-Lapointe, L A Reynolds, E M Brown, A Valdez-Salazar, P Morán-Silva, L Rojas-Velázquez, E Morien, L W Parfrey, M Jin, J Walter, J Torres, M C Arrieta, C Ximénez-García, B B Finlay
Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation...
May 2018: MSystems
https://www.readbyqxmd.com/read/29946568/modeling-the-pseudomonas-sulfur-regulome-by-quantifying-the-storage-and-communication-of-information
#8
Peter E Larsen, Sarah Zerbs, Philip D Laible, Frank R Collart, Peter Korajczyk, Yang Dai, Philippe Noirot
Bacteria are not simply passive consumers of nutrients or merely steady-state systems. Rather, bacteria are active participants in their environments, collecting information from their surroundings and processing and using that information to adapt their behavior and optimize survival. The bacterial regulome is the set of physical interactions that link environmental information to the expression of genes by way of networks of sensors, transporters, signal cascades, and transcription factors. As bacteria cannot have one dedicated sensor and regulatory response system for every possible condition that they may encounter, the sensor systems must respond to a variety of overlapping stimuli and collate multiple forms of information to make "decisions" about the most appropriate response to a specific set of environmental conditions...
May 2018: MSystems
https://www.readbyqxmd.com/read/29896568/metagenomics-reveals-the-influence-of-land-use-and-rain-on-the-benthic-microbial-communities-in-a-tropical-urban-waterway
#9
Gourvendu Saxena, Suparna Mitra, Ezequiel M Marzinelli, Chao Xie, Toh Jun Wei, Peter D Steinberg, Rohan B H Williams, Staffan Kjelleberg, Federico M Lauro, Sanjay Swarup
Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities...
May 2018: MSystems
https://www.readbyqxmd.com/read/29896567/genomics-of-the-uncultivated-periodontitis-associated-bacterium-tannerella-sp-bu045-oral-taxon-808
#10
Clifford J Beall, Alisha G Campbell, Ann L Griffen, Mircea Podar, Eugene J Leys
Despite decades of research into the human oral microbiome, many species remain uncultivated. The technique of single-cell whole-genome amplification and sequencing provides a means of deriving genome sequences for species that can be informative on biological function and suggest pathways to cultivation. Tannerella forsythia has long been known to be highly associated with chronic periodontitis and to cause periodontitis-like symptoms in experimental animals, and Tannerella sp. BU045 (human oral taxon 808) is an uncultivated relative of this organism...
May 2018: MSystems
https://www.readbyqxmd.com/read/29896566/intermittent-hypoxia-and-hypercapnia-a-hallmark-of-obstructive-sleep-apnea-alters-the-gut-microbiome-and-metabolome
#11
Anupriya Tripathi, Alexey V Melnik, Jin Xue, Orit Poulsen, Michael J Meehan, Gregory Humphrey, Lingjing Jiang, Gail Ackermann, Daniel McDonald, Dan Zhou, Rob Knight, Pieter C Dorrestein, Gabriel G Haddad
Obstructive sleep apnea (OSA) is a common disorder characterized by episodic obstruction to breathing due to upper airway collapse during sleep. Because of the episodic airway obstruction, intermittently low O2 (hypoxia) and high CO2 (hypercapnia) ensue. OSA has been associated with adverse cardiovascular and metabolic outcomes, although data regarding potential causal pathways are still evolving. As changes in inspired O2 and CO2 can affect the ecology of the gut microbiota and the microbiota has been shown to contribute to various cardiometabolic disorders, we hypothesized that OSA alters the gut ecosystem, which, in turn, exacerbates the downstream physiological consequences...
May 2018: MSystems
https://www.readbyqxmd.com/read/29854954/heterotroph-interactions-alter-prochlorococcus-transcriptome-dynamics-during-extended-periods-of-darkness
#12
Steven J Biller, Allison Coe, Sara E Roggensack, Sallie W Chisholm
Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus , grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness-a condition that cells would experience when mixed below the ocean's euphotic zone...
May 2018: MSystems
https://www.readbyqxmd.com/read/29854953/environmental-sources-of-bacteria-differentially-influence-host-associated-microbial-dynamics
#13
Cesar Cardona, Simon Lax, Peter Larsen, Brent Stephens, Jarrad Hampton-Marcell, Christian F Edwardson, Chris Henry, Bill Van Bonn, Jack A Gilbert
Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply...
May 2018: MSystems
https://www.readbyqxmd.com/read/29795809/american-gut-an-open-platform-for-citizen-science-microbiome-research
#14
Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples...
May 2018: MSystems
https://www.readbyqxmd.com/read/29795799/crowdsourcing-our-national-gut
#15
Laura E Grieneisen, Ran Blekhman
The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle. To address this problem, McDonald et al. (mSystems 3:e00031-18, 2018, https://doi.org/10.1128/mSystems.00031-18) present the first set of results from the American Gut Project, a citizen science-based data set currently comprised of over 10,000 gut microbiome samples and associated life history data...
May 2018: MSystems
https://www.readbyqxmd.com/read/29795788/viromic-analysis-of-wastewater-input-to-a-river-catchment-reveals-a-diverse-assemblage-of-rna-viruses
#16
Evelien M Adriaenssens, Kata Farkas, Christian Harrison, David L Jones, Heather E Allison, Alan J McCarthy
Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes...
May 2018: MSystems
https://www.readbyqxmd.com/read/29795787/interaction-between-host-micrornas-and-the-gut-microbiota-in-colorectal-cancer
#17
Ce Yuan, Michael B Burns, Subbaya Subramanian, Ran Blekhman
Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues...
May 2018: MSystems
https://www.readbyqxmd.com/read/29766049/interleukin-1%C3%AE-deficient-mice-have-an-altered-gut-microbiota-leading-to-protection-from-dextran-sodium-sulfate-induced-colitis
#18
Moran Nunberg, Nir Werbner, Hadar Neuman, Marina Bersudsky, Alex Braiman, Moshe Ben-Shoshan, Meirav Ben Izhak, Yoram Louzoun, Ron N Apte, Elena Voronov, Omry Koren
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory disorders of the intestine, with as-yet-unclear etiologies, affecting over a million people in the United States alone. With the emergence of microbiome research, numerous studies have shown a connection between shifts in the gut microbiota composition (dysbiosis) and patterns of IBD development. In a previous study, we showed that interleukin 1α (IL-1α) deficiency in IL-1α knockout (KO) mice results in moderate dextran sodium sulfate (DSS)-induced colitis compared to that of wild-type (WT) mice, characterized by reduced inflammation and complete healing, as shown by parameters of weight loss, disease activity index (DAI) score, histology, and cytokine expression...
May 2018: MSystems
https://www.readbyqxmd.com/read/29719872/shi7-is-a-self-learning-pipeline-for-multipurpose-short-read-dna-quality-control
#19
Gabriel A Al-Ghalith, Benjamin Hillmann, Kaiwei Ang, Robin Shields-Cutler, Dan Knights
Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation...
May 2018: MSystems
https://www.readbyqxmd.com/read/29719871/a-prospective-metagenomic-and-metabolomic-analysis-of-the-impact-of-exercise-and-or-whey-protein-supplementation-on-the-gut-microbiome-of-sedentary-adults
#20
Owen Cronin, Wiley Barton, Peter Skuse, Nicholas C Penney, Isabel Garcia-Perez, Eileen F Murphy, Trevor Woods, Helena Nugent, Aine Fanning, Silvia Melgar, Eanna C Falvey, Elaine Holmes, Paul D Cotter, Orla O'Sullivan, Michael G Molloy, Fergus Shanahan
Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption...
May 2018: MSystems
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