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"Microbial ecology"

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https://www.readbyqxmd.com/read/28106010/models-of-life-epigenetics-diversity-cycles
#1
Kim Sneppen
This review emphasize aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is minimal rules to sustain specific states of a complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that later return to new metastable states...
January 20, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28100229/surveillance-of-life-long-antibiotics-a-review-of-antibiotic-prescribing-practices-in-an-australian-healthcare-network
#2
Jillian S Y Lau, Christopher Kiss, Erika Roberts, Kylie Horne, Tony M Korman, Ian Woolley
BACKGROUND: The rise of antimicrobial use in the twentieth century has significantly reduced morbidity due to infection, however it has also brought with it the rise of increasing resistance. Some patients are on prolonged, if not "life-long" course of antibiotics. The reasons for this are varied, and include non-infectious indications. We aimed to study the characteristics of this potential source of antibiotic resistance, by exploring the antibiotic dispensing practices and describing the population of patients on long-term antibiotic therapy...
January 18, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/28088532/comparison-of-an-anaerobic-feed-and-split-anaerobic-aerobic-feed-on-granular-sludge-development-performance-and-ecology
#3
Benjamin J Thwaites, Petra Reeve, Nirmala Dinesh, Michael D Short, Ben van den Akker
The retrofitting of existing wastewater sequencing batch reactors (SBRs) to select for rapid-settling aerobic granular sludge (AGS) over floc-based conventional activated sludge (CAS), could be a viable option to decrease reactor cycle time and increase hydraulic capacity. Successful CAS-to-AGS conversion has previously been shown to be highly dependent on having a dedicated anaerobic feed, which presents additional engineering challenges when retrofitting SBRs. In this study we compared the performance of a split anaerobic-aerobic (An-Aer) feed with that of a traditional dedicated anaerobic feed regarding AGS formation and stability, nitrogen removal performance and microbial ecology...
December 29, 2016: Chemosphere
https://www.readbyqxmd.com/read/28088423/effects-of-rumen-protected-capsicum-oleoresin-on-productivity-and-responses-to-a-glucose-tolerance-test-in-lactating-dairy-cows
#4
J Oh, M Harper, F Giallongo, D M Bravo, E H Wall, A N Hristov
The objective of this experiment was to investigate the effects of rumen-protected Capsicum oleoresin (RPC) supplementation on feed intake, milk yield and composition, nutrient utilization, fecal microbial ecology, and responses to a glucose tolerance test in lactating dairy cows. Nine multiparous Holstein cows were used in a replicated 3 × 3 Latin square design balanced for residual effects with three 28-d periods. Each period consisted of 14 d for adaptation and 14 d for data collection and sampling. Treatments were 0 (control), 100, and 200 mg RPC/cow per day...
January 11, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28070331/effects-of-bacillus-subtilis-csl2-on-the-composition-and-functional-diversity-of-the-faecal-microbiota-of-broiler-chickens-challenged-with-salmonella-gallinarum
#5
Ju Kyoung Oh, Edward Alain B Pajarillo, Jong Pyo Chae, In Ho Kim, Dong Soo Yang, Dae-Kyung Kang
BACKGROUND: The chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with Bacillus subtilis CSL2 were evaluated in broilers challenged and unchallenged with Salmonella Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed. RESULTS: The Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period...
2017: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/28065710/ecoimmunology-and-microbial-ecology-contributions-to-avian-behavior-physiology-and-life-history
#6
REVIEW
Jessica K Evans, Katherine L Buchanan, Simon C Griffith, Kirk C Klasing, BriAnne Addison
Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories...
January 5, 2017: Hormones and Behavior
https://www.readbyqxmd.com/read/28062463/ymc-2011-a-temperate-phage-of-streptococcus-salivarius-57-i
#7
Wen-Chun Chou, Szu-Chuan Huang, Cheng-Hsun Chiu, Yi-Ywan M Chen
: Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally with an estimated copy number of 3 to 4...
January 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28059627/structural-and-functional-alterations-in-the-colonic-microbiome-of-the-rat-in-a-model-of-stress-induced-irritable-bowel-syndrome
#8
Nicolaas H Fourie, Dan Wang, Sarah K Abey, Amy L Creekmore, Shuangsong Hong, Christiana G Martin, John W Wiley, Wendy A Henderson
Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data...
January 6, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28057476/operative-treatment-of-early-infection-after-internal-fixation-of-limb-fractures-exclusive-of-severe-open-fractures
#9
REVIEW
P Bonnevialle
Early infection after open reduction and internal fixation (ORIF) of a limb bone is defined as bacteriologically documented, deep and/or superficial surgical-site infection (SSI) diagnosed within 6months after the surgical procedure. This interval is arbitrarily considered sufficient to obtain fracture healing. The treatment of early infection after ORIF should be decided by a multidisciplinary team. The principles are the same as for revision arthroplasty. Superficial SSIs should be differentiated from deep SSIs, based on the results of bacteriological specimens collected using flawless technique...
January 2, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#10
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28042698/geochemically-distinct-carbon-isotope-distributions-in-allochromatium-vinosum-dsm-180-t-grown-photoautotrophically-and-photoheterotrophically
#11
T Tang, W Mohr, S R Sattin, D R Rogers, P R Girguis, A Pearson
Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180(T) ...
January 1, 2017: Geobiology
https://www.readbyqxmd.com/read/28034543/using-soil-microbial-inoculations-to-enhance-substrate-performance-on-extensive-green-roofs
#12
Chloe J Molineux, Alan C Gange, Darryl J Newport
Green roofs are increasing in popularity in the urban environment for their contribution to green infrastructure; but their role for biodiversity is not often a design priority. Maximising biodiversity will impact positively on ecosystem services and is therefore fundamental for achieving the greatest benefits from green roofs. Extensive green roofs are lightweight systems generally constructed with a specialised growing medium that tends to be biologically limited and as such can be a harsh habitat for plants to thrive in...
December 26, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#13
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28028456/seqenv-linking-sequences-to-environments-through-text-mining
#14
Lucas Sinclair, Umer Z Ijaz, Lars Juhl Jensen, Marco J L Coolen, Cecile Gubry-Rangin, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis
Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context...
2016: PeerJ
https://www.readbyqxmd.com/read/28025470/virologists-are-symbionts-in-microbial-ecology
#15
Ken Takai
No abstract text is available yet for this article.
2016: Microbes and Environments
https://www.readbyqxmd.com/read/28012222/temporal-dynamics-of-microbial-communities-in-microcosms-in-response-to-pollutants
#16
Shuo Jiao, Zhengqing Zhang, Fan Yang, Yanbing Lin, Weimin Chen, Gehong Wei
Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analyzed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane, and phenanthrene + n-octadecane + CdCl2 )...
December 24, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27999158/disturbance-regimes-predictably-alter-diversity-in-an-ecologically-complex-bacterial-system
#17
Sean M Gibbons, Monika Scholz, Alan L Hutchison, Aaron R Dinner, Jack A Gilbert, Maureen L Coleman
: Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient...
December 20, 2016: MBio
https://www.readbyqxmd.com/read/27997146/silver-sink-effect-of-humic-acid-on-bacterial-surface-colonization-in-the-presence-of-silver-ions-and-nanoparticles
#18
Alex J Bertuccio, Robert D Tilton
Silver nanoparticles (AgNPs) released from consumer products may enter the environment and possibly harm microbial communities. Prior research showed that surface-adherent AgNPs inhibit bacterial surface colonization, a precursor to biofilm formation, only when planktonic bacterial inoculum concentrations are less than a threshold level ( Wirth and co-workers, J. Colloid Interface Sci. 2016 , 467 , 17 - 27 ). This inoculum effect is due to a decrease in free silver ion concentration associated with sublethal binding to bacteria...
January 9, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/27984802/microbial-soil-community-analyses-for-forensic-science-application-to-a-blind-test
#19
Sandrine Demanèche, Leif Schauser, Lorna Dawson, Laure Franqueville, Pascal Simonet
Soil complexity, heterogeneity and transferability make it valuable in forensic investigations to help obtain clues as to the origin of an unknown sample, or to compare samples from a suspect or object with samples collected at a crime scene. In a few countries, soil analysis is used in matters from site verification to estimates of time after death. However, up to date the application or use of soil information in criminal investigations has been limited. In particular, comparing bacterial communities in soil samples could be a useful tool for forensic science...
December 9, 2016: Forensic Science International
https://www.readbyqxmd.com/read/27984592/inferring-aggregated-functional-traits-from-metagenomic-data-using-constrained-non-negative-matrix-factorization-application-to-fiber-degradation-in-the-human-gut-microbiota
#20
Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche
Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes...
December 2016: PLoS Computational Biology
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