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Gautam dantas

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https://www.readbyqxmd.com/read/29909042/close-encounters-of-three-kinds-bacteriophages-commensal-bacteria-and-host-immunity
#1
REVIEW
Eric C Keen, Gautam Dantas
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome...
June 13, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29713061/shared-strategies-for-%C3%AE-lactam-catabolism-in-the-soil-microbiome
#2
Terence S Crofts, Bin Wang, Aaron Spivak, Tara A Gianoulis, Kevin J Forsberg, Molly K Gibson, Lauren A Johnsky, Stacey M Broomall, C Nicole Rosenzweig, Evan W Skowronski, Henry S Gibbons, Morten O A Sommer, Gautam Dantas
The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate...
June 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29691222/checkpoint-checkmate-microbiota-modulation-of-cancer-immunotherapy
#3
Eric C Keen, Terence S Crofts, Gautam Dantas
No abstract text is available yet for this article.
April 24, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29522743/multiscale-evolutionary-dynamics-of-host-associated-microbiomes
#4
REVIEW
Aura Ferreiro, Nathan Crook, Andrew J Gasparrini, Gautam Dantas
The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem...
March 8, 2018: Cell
https://www.readbyqxmd.com/read/29496594/bla-imp-27-on-transferable-plasmids-in-proteus-mirabilis-and-providencia-rettgeri
#5
R F Potter, M A Wallace, A R McMullen, J Prusa, C L Stallings, C A D Burnham, G Dantas
OBJECTIVES: A carbapenem-resistant Providencia rettgeri (PR1) isolate was recovered from a wound infection in Missouri, USA. This isolate possessed an EDTA-inhibitable carbapenemase that was unidentified using the Xpert CARBA-R assay. Our objective was to elucidate the molecular determinant of carbapenem resistance in this isolate. We then sought to test the transmissibility of blaIMP-27 loci in clinical P. rettgeri and Proteus mirabilis isolates. METHODS: In October 2016 the novel ambler Class B carbapenemase blaIMP-27 , was reported in two different Proteus mirabilis (PM185 and PM187) isolates...
March 1, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29146837/draft-genome-sequence-of-the-naturally-competent-bacillus-simplex-strain-wy10
#6
Eric C Keen, Valery V Bliskovsky, Sankar L Adhya, Gautam Dantas
We sequenced a naturally competent bacterial isolate, WY10, cultured from a Wyoming soil sample. Sequence analysis revealed that WY10 is a novel strain of Bacillus simplex To our knowledge, WY10 is the first B. simplex strain to be characterized as naturally competent for DNA uptake by transformation.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29051234/draft-genome-sequence-of-a-salmonella-enterica-serovar-typhi-strain-resistant-to-fourth-generation-cephalosporin-and-fluoroquinolone-antibiotics
#7
Danish Gul, Robert F Potter, Hurmat Riaz, Shifa Tariq Ashraf, Meghan A Wallace, Tehmina Munir, Amjad Ali, C A Burnham, Gautam Dantas, Saadia Andleeb
Typhoid is endemic in developing countries. We report here the first draft genome sequence of a Salmonella enterica serovar Typhi clinical isolate from Pakistan exhibiting resistance to cefepime (a fourth-generation cephalosporin) and fluoroquinolone antibiotics, two of the last-generation therapies against this pathogen. The genome is ~4.8 Mb, with two putative plasmids.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798166/draft-genome-sequences-of-three-%C3%AE-lactam-catabolizing-soil-proteobacteria
#8
Terence S Crofts, Bin Wang, Aaron Spivak, Tara A Gianoulis, Kevin J Forsberg, Molly K Gibson, Lauren A Johnsky, Stacey M Broomall, C Nicole Rosenzweig, Evan W Skowronski, Henry S Gibbons, Morten O A Sommer, Gautam Dantas
Most antibiotics are derived from the soil, but their catabolism there, which is necessary to close the antibiotic carbon cycle, remains uncharacterized. We report the first draft genome sequences of soil Proteobacteria identified for subsisting solely on β-lactams as their carbon sources. The genomes encode multiple β-lactamases, although their antibiotic catabolic pathways remain enigmatic.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28756664/structural-and-functional-survey-of-environmental-aminoglycoside-acetyltransferases-reveals-functionality-of-resistance-enzymes
#9
Zhiyu Xu, Peter J Stogios, Andrew T Quaile, Kevin J Forsberg, Sanket Patel, Tatiana Skarina, Scott Houliston, Cheryl Arrowsmith, Gautam Dantas, Alexei Savchenko
Aminoglycoside N-acetyltransferases (AACs) confer resistance against the clinical use of aminoglycoside antibiotics. The origin of AACs can be traced to environmental microbial species representing a vast reservoir for new and emerging resistance enzymes, which are currently undercharacterized. Here, we performed detailed structural characterization and functional analyses of four metagenomic AAC (meta-AACs) enzymes recently identified in a survey of agricultural and grassland soil microbiomes ( Forsberg et al...
September 8, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28729267/draft-genome-sequence-of-the-bla-oxa-436-and-bla-ndm-1-harboring-shewanella-putrefaciens-sa70-isolate
#10
Robert F Potter, Alaric W D'Souza, Meghan A Wallace, Angela Shupe, Sanket Patel, Danish Gul, Jennie H Kwon, Saadia Andleeb, C A Burnham, Gautam Dantas
We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cultured from the sink handle of a Pakistan hospital room. Assembly annotation indicates that the isolate has a chromosomal bla OXA-436 carbapenemase and a plasmid-borne bla NDM-1 gene. To our knowledge, this is the first report of a Shewanella species harboring bla NDM .
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28481346/plasticity-dynamics-and-inhibition-of-emerging-tetracycline-resistance-enzymes
#11
Jooyoung Park, Andrew J Gasparrini, Margaret R Reck, Chanez T Symister, Jennifer L Elliott, Joseph P Vogel, Timothy A Wencewicz, Gautam Dantas, Niraj H Tolia
Although tetracyclines are an important class of antibiotics for use in agriculture and the clinic, their efficacy is threatened by increasing resistance. Resistance to tetracyclines can occur through efflux, ribosomal protection, or enzymatic inactivation. Surprisingly, tetracycline enzymatic inactivation has remained largely unexplored, despite providing the distinct advantage of antibiotic clearance. The tetracycline destructases are a recently discovered family of tetracycline-inactivating flavoenzymes from pathogens and soil metagenomes that have a high potential for broad dissemination...
July 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28392565/next-generation-approaches-to-understand-and-combat-the-antibiotic-resistome
#12
REVIEW
Terence S Crofts, Andrew J Gasparrini, Gautam Dantas
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities...
July 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/27965630/evaluation-of-machine-learning-and-rules-based-approaches-for-predicting-antimicrobial-resistance-profiles-in-gram-negative-bacilli-from-whole-genome-sequence-data
#13
Mitchell W Pesesky, Tahir Hussain, Meghan Wallace, Sanket Patel, Saadia Andleeb, Carey-Ann D Burnham, Gautam Dantas
The time-to-result for culture-based microorganism recovery and phenotypic antimicrobial susceptibility testing necessitates initial use of empiric (frequently broad-spectrum) antimicrobial therapy. If the empiric therapy is not optimal, this can lead to adverse patient outcomes and contribute to increasing antibiotic resistance in pathogens. New, more rapid technologies are emerging to meet this need. Many of these are based on identifying resistance genes, rather than directly assaying resistance phenotypes, and thus require interpretation to translate the genotype into treatment recommendations...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27912842/the-rapid-spread-of-carbapenem-resistant-enterobacteriaceae
#14
REVIEW
Robert F Potter, Alaric W D'Souza, Gautam Dantas
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27873261/functional-metagenomics-to-study-antibiotic-resistance
#15
Manish Boolchandani, Sanket Patel, Gautam Dantas
The construction and screening of metagenomic expression libraries has great potential to identify novel genes and their functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27768825/genomic-and-functional-techniques-to-mine-the-microbiome-for-novel-antimicrobials-and-antimicrobial-resistance-genes
#16
REVIEW
Boahemaa Adu-Oppong, Andrew J Gasparrini, Gautam Dantas
Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance...
January 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27704542/contextual-organismality-beyond-pattern-to-process-in-the-emergence-of-organisms
#17
Samuel L Díaz-Muñoz, Amy M Boddy, Gautam Dantas, Christopher M Waters, Judith L Bronstein
Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms...
December 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27572443/developmental-dynamics-of-the-preterm-infant-gut-microbiota-and-antibiotic-resistome
#18
Molly K Gibson, Bin Wang, Sara Ahmadi, Carey-Ann D Burnham, Phillip I Tarr, Barbara B Warner, Gautam Dantas
Development of the preterm infant gut microbiota is emerging as a critical research priority(1). Since preterm infants almost universally receive early and often extended antibiotic therapy(2), it is important to understand how these interventions alter gut microbiota development(3-6). Analysis of 401 stools from 84 longitudinally sampled preterm infants demonstrates that meropenem, cefotaxime and ticarcillin-clavulanate are associated with significantly reduced species richness. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness, but these can be predicted with 85% accuracy based on the relative abundance of only two bacterial species and two antibiotic resistance (AR) genes at treatment initiation...
March 7, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27472377/antibiotic-perturbation-of-the-preterm-infant-gut-microbiome-and-resistome
#19
REVIEW
Andrew J Gasparrini, Terence S Crofts, Molly K Gibson, Phillip I Tarr, Barbara B Warner, Gautam Dantas
The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth...
September 2, 2016: Gut Microbes
https://www.readbyqxmd.com/read/27276888/transcriptomic-analysis-illuminates-genes-involved-in-chlorophyll-synthesis-after-nitrogen-starvation-in-acaryochloris-sp-ccmee-5410
#20
Aki Yoneda, Bruce J Wittmann, Jeremy D King, Robert E Blankenship, Gautam Dantas
Acaryochloris species are a genus of cyanobacteria that utilize chlorophyll (chl) d as their primary chlorophyll molecule during oxygenic photosynthesis. Chl d allows Acaryochloris to harvest red-shifted light, which gives them the ability to live in filtered light environments that are depleted in visible light. Although genomes of multiple Acaryochloris species have been sequenced, their analysis has not revealed how chl d is synthesized. Here, we demonstrate that Acaryochloris sp. CCMEE 5410 cells undergo chlorosis by nitrogen depletion and exhibit robust regeneration of chl d by nitrogen repletion...
August 2016: Photosynthesis Research
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