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Rob Knight

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https://www.readbyqxmd.com/read/28428981/correction-for-gonzalez-et-al-migraines-are-correlated-with-higher-levels-of-nitrate-nitrite-and-nitric-oxide-reducing-oral-microbes-in-the-american-gut-project-cohort
#1
Antonio Gonzalez, Embriette Hyde, Naseer Sangwan, Jack A Gilbert, Erik Viirre, Rob Knight
[This corrects the article DOI: 10.1128/mSystems.00105-16.].
March 2017: MSystems
https://www.readbyqxmd.com/read/28421042/mosquito-microbiome-dynamics-a-background-for-prevalence-and-seasonality-of-west-nile-virus
#2
Eva Novakova, Douglas C Woodhams, Sonia M Rodríguez-Ruano, Robert M Brucker, Jonathan W Leff, Amin Maharaj, Amnon Amir, Rob Knight, James Scott
Symbiotic microbial communities augment host phenotype, including defense against pathogen carriage and infection. We sampled the microbial communities in 11 adult mosquito host species from six regions in southern Ontario, Canada over 3 years. Of the factors examined, we found that mosquito species was the largest driver of the microbiota, with remarkable phylosymbiosis between host and microbiota. Seasonal shifts of the microbiome were consistently repeated over the 3-year period, while region had little impact...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28405197/mass-spectrometry-based-molecular-3d-cartography-of-plant-metabolites
#3
Dimitrios J Floros, Daniel Petras, Clifford A Kapono, Alexey V Melnik, Tie-Jun Ling, Rob Knight, Pieter C Dorrestein
Plants play an essential part in global carbon fixing through photosynthesis and are the primary food and energy source for humans. Understanding them thoroughly is therefore of highest interest for humanity. Advances in DNA and RNA sequencing and in protein and metabolite analysis allow the systematic description of plant composition at the molecular level. With imaging mass spectrometry, we can now add a spatial level, typically in the micrometer-to-centimeter range, to their compositions, essential for a detailed molecular understanding...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28375652/the-microbiome-and-human-biology
#4
Rob Knight, Chris Callewaert, Clarisse Marotz, Embriette R Hyde, Justine W Debelius, Daniel McDonald, Mitchell L Sogin
Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries...
March 20, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28366290/microbiome-tools-for-forensic-science
#5
REVIEW
Jessica L Metcalf, Zhenjiang Z Xu, Amina Bouslimani, Pieter Dorrestein, David O Carter, Rob Knight
Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system...
March 30, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28333945/environmental-reservoirs-of-pathogenic-mycobacteria-across-the-ethiopian-biogeographical-landscape
#6
Hayley C King, Tanya Khera-Butler, Phillip James, Brian B Oakley, Girume Erenso, Abraham Aseffa, Rob Knight, Elizabeth M Wellington, Orin Courtenay
The Mycobacterium genus comprises over one-hundred-and-fifty recognised species, the majority of which reside in the environment and many of which can be pathogenic to mammals. Some species of environmental mycobacteria may interfere with BCG vaccination efficacy and in tuberculin test interpretation. Examining biogeographic trends in the distribution of members of the mycobacteria across a number of physicochemical and spatial gradients in soil and water environments across Ethiopia using oligotyping identified differential distributions of pathogenic and significant species...
2017: PloS One
https://www.readbyqxmd.com/read/28289733/correcting-for-microbial-blooms-in-fecal-samples-during-room-temperature-shipping
#7
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Justine Debelius, James T Morton, Embriette Hyde, Adam Robbins-Pianka, Rob Knight
The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289731/deblur-rapidly-resolves-single-nucleotide-community-sequence-patterns
#8
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Evguenia Kopylova, James T Morton, Zhenjiang Zech Xu, Eric P Kightley, Luke R Thompson, Embriette R Hyde, Antonio Gonzalez, Rob Knight
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms...
March 2017: MSystems
https://www.readbyqxmd.com/read/28279336/a-microbiome-foundation-for-the-study-of-crohn-s-disease
#9
Dirk Gevers, Subra Kugathasan, Dan Knights, Aleksandar D Kostic, Rob Knight, Ramnik J Xavier
Our 2014 study published in Cell Host & Microbe, "The Treatment-Naive Microbiome in New-Onset Crohn's Disease," was designed to improve our understanding of the microbiome's role in Crohn's disease by studying a unique, well-suited cohort and sample set. This commentary provides a hindsight perspective of this original study as well as future outlook.
March 8, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28268215/randomised-comparison-of-a-novel-buprenorphine-oral-lyophilisate-versus-existing-buprenorphine-sublingual-tablets-in-opioid-dependent-patients-a-first-in-patient-phase-ii-randomised-open-label-safety-study
#10
John Strang, Kylie Reed, Karolina Bogdanowicz, James Bell, Rob van der Waal, Jenny Keen, Pete Beavan, Shelagh Baillie, Alastair Knight
AIMS: To test the safety of new buprenorphine oral lyophilisate wafer ("bup-lyo") versus standard sub-lingual buprenorphine ("bup-SL"). DESIGN: Randomised (2:1) open-label study; opioid-dependent subjects; subsequent partial cross-over. SETTINGS: Specialised clinical trials facility and addictions treatment facility. PARTICIPANTS: Opioid-dependent subjects (n = 36) commencing buprenorphine maintenance (personalised dose-titration) including patients co-using alcohol, cocaine and benzodiazepines (below thresholds)...
March 8, 2017: European Addiction Research
https://www.readbyqxmd.com/read/28258145/comparison-of-fecal-collection-methods-for-microbiota-studies-in-bangladesh
#11
Emily Vogtmann, Jun Chen, Muhammad G Kibriya, Yu Chen, Tariqul Islam, Mahbubul Eunes, Alauddin Ahmed, Jabun Naher, Anisur Rahman, Amnon Amir, Jianxin Shi, Christian C Abnet, Heidi Nelson, Rob Knight, Nicholas Chia, Habibul Ahsan, Rashmi Sinha
To our knowledge, fecal microbiota collection methods have not been evaluated in low and middle income countries. Therefore, we evaluated five different fecal sample collections methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, post-development fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes...
March 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28253908/normalization-and-microbial-differential-abundance-strategies-depend-upon-data-characteristics
#12
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/28251186/uncovering-the-horseshoe-effect-in-microbial-analyses
#13
James T Morton, Liam Toran, Anna Edlund, Jessica L Metcalf, Christian Lauber, Rob Knight
The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate-a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features...
January 2017: MSystems
https://www.readbyqxmd.com/read/28195358/parkinson-s-disease-and-parkinson-s-disease-medications-have-distinct-signatures-of-the-gut-microbiome
#14
Erin M Hill-Burns, Justine W Debelius, James T Morton, William T Wissemann, Matthew R Lewis, Zachary D Wallen, Shyamal D Peddada, Stewart A Factor, Eric Molho, Cyrus P Zabetian, Rob Knight, Haydeh Payami
BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE: The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. METHODS: A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool...
February 14, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28193877/origin-of-microbial-biomineralization-and-magnetotaxis-during-the-archean
#15
Wei Lin, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28191884/dynamics-of-the-human-gut-microbiome-in-inflammatory-bowel-disease
#16
Jonas Halfvarson, Colin J Brislawn, Regina Lamendella, Yoshiki Vázquez-Baeza, William A Walters, Lisa M Bramer, Mauro D'Amato, Ferdinando Bonfiglio, Daniel McDonald, Antonio Gonzalez, Erin E McClure, Mitchell F Dunklebarger, Rob Knight, Janet K Jansson
Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease. Although IBD is dynamic, microbiome studies have primarily focused on single time points or a few individuals...
February 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28152560/transcriptional-characterization-of-vibrio-fischeri-during-colonization-of-juvenile-euprymna-scolopes
#17
Luke R Thompson, Kiel Nikolakakis, Shu Pan, Jennifer Reed, Rob Knight, Edward G Ruby
The marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and the establishment of this association involves a number of signaling pathways and transcriptional responses between both partners. We report here the first full RNA-Seq dataset representing host-associated V. fischeri cells from colonized juvenile E. scolopes, as well as comparative transcriptomes under both laboratory and simulated marine planktonic conditions. These data elucidate the broad transcriptional changes that these bacteria undergo during the early stages of symbiotic colonization...
February 2, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28144630/balance-trees-reveal-microbial-niche-differentiation
#18
James T Morton, Jon Sanders, Robert A Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A Navas-Molina, Se Jin Song, Jessica L Metcalf, Embriette R Hyde, Manuel Lladser, Pieter C Dorrestein, Rob Knight
Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others...
January 2017: MSystems
https://www.readbyqxmd.com/read/28124727/patterns-in-gut-microbiota-similarity-associated-with-degree-of-sociality-among-sex-classes-of-a-neotropical-primate
#19
Katherine R Amato, Sarie Van Belle, Anthony Di Fiore, Alejandro Estrada, Rebecca Stumpf, Bryan White, Karen E Nelson, Rob Knight, Steven R Leigh
Studies of human and domestic animal models indicate that related individuals and those that spend the most time in physical contact typically have more similar gut microbial communities. However, few studies have examined these factors in wild mammals where complex social dynamics and a variety of interacting environmental factors may impact the patterns observed in controlled systems. Here, we explore the effect of host kinship and time spent in social contact on the gut microbiota of wild, black howler monkeys (Alouatta pigra)...
January 26, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28081445/bringing-the-dynamic-microbiome-to-life-with-animations
#20
Yoshiki Vázquez-Baeza, Antonio Gonzalez, Larry Smarr, Daniel McDonald, James T Morton, Jose A Navas-Molina, Rob Knight
Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We have now improved EMPeror to create interactive animations that connect successive samples to highlight patterns over time.
January 11, 2017: Cell Host & Microbe
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