keyword
MENU ▼
Read by QxMD icon Read
search

"Microbial ecology"

keyword
https://www.readbyqxmd.com/read/27924593/analysis-of-16s-rrna-gene-amplicon-sequences-using-the-qiime-software-package
#1
Blair Lawley, Gerald W Tannock
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#2
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27904402/microbiological-quality-and-variability-of-natural-microbiota-in-croatian-cheese-maturing-in-lambskin-sacks
#3
Jadranka Frece, Marija Vrdoljak, Mija Filipčić, Marko Jelić, Iva Čanak, Željko Jakopović, Jelka Pleadin, Ivana Gobin, Tibela Landeka Dragičević, Ksenija Markov
As in the traditional production of cheese in lambskin sacks raw cow's or sheep's milk is mostly used, the purpose of this study is to see how the production affects the microbiological quality of the cheese. To do that, we tested 39 samples of raw cow's and sheep's milk, curd, ripened cheese (15, 30 and 45 days) and lambskin sacks for native microbial population. Two-thirds of the milk, curd and cheese samples had higher counts of staphylococci and enterobacteria than permitted by regulations. Not a single sample had Salmonella and Listeria monocytogenes, but we did find Escherichia coli in sheep's milk and cheese, and yeast and mould in both types of milk and cheese...
June 2016: Food Technology and Biotechnology
https://www.readbyqxmd.com/read/27903594/chronic-rhinosinusitis-and-the-evolving-understanding-of-microbial-ecology-in-chronic-inflammatory-mucosal-disease
#4
REVIEW
Michael Hoggard, Brett Wagner Mackenzie, Ravi Jain, Michael W Taylor, Kristi Biswas, Richard G Douglas
Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation...
January 2017: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#5
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27888456/soil-ph-and-electrical-conductivity-are-key-edaphic-factors-shaping-bacterial-communities-of-greenhouse-soils-in-korea
#6
Jeong Myeong Kim, An-Sung Roh, Seung-Chul Choi, Eun-Jeong Kim, Moon-Tae Choi, Byung-Koo Ahn, Sun-Kuk Kim, Young-Han Lee, Jae-Ho Joa, Seong-Soo Kang, Shin Ae Lee, Jae-Hyung Ahn, Jaekyeong Song, Hang-Yeon Weon
Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis...
December 2016: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/27881419/oral-administration-of-a-select-mixture-of-bacillus-probiotics-affects-the-gut-microbiota-and-goblet-cell-function-in-newly-weaned-muc4-resistant-pigs-following-escherichia-coli-challenge
#7
Wei Zhang, Yao-Hong Zhu, Dong Zhou, Qiong Wu, Dan Song, Johan Dicksved, Jiu-Feng Wang
: Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS-mix) were orally administered to MUC4 resistant piglets for 1 week before the F4-expressing ETEC strain (F4(+) ETEC) challenge. The luminal contents were collected from the mucosa of colon on day 8 after F4(+) ETEC challenge. BLS-mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium and Sporobacter populations...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27869357/the-impact-of-endoscopic-sinus-surgery-on-paranasal-physiology-in-simulated-sinus-cavities
#8
Ravi Jain, Haribalan Kumar, Merryn Tawhai, Richard Douglas
BACKGROUND: Surgery improves symptoms for the majority of chronic rhinosinusitis (CRS) patients; however, physiological changes in the sinus cavities remain poorly characterized. Direct measurement of changes in airflow, pressure, temperature, humidity, and intranasal spray distribution following surgery is technically challenging. Accordingly, we have used computational fluid dynamic modeling to quantify how these parameters change postoperatively. METHODS: Computed tomography images from a normal control, a patient with CRS preoperatively and postoperatively, and a patient following an endoscopic Lothrop procedure (ELP) were used to create 4 three-dimensional models of the sinus cavities...
November 21, 2016: International Forum of Allergy & Rhinology
https://www.readbyqxmd.com/read/27862531/gut-microbial-ecology-of-lizards-insights-into-diversity-in-the-wild-effects-of-captivity-variation-across-gut-regions-and-transmission
#9
Kevin D Kohl, Antonio Brun, Melisa Magallanes, Joshua Brinkerhoff, Alejandro Laspiur, Juan Carlos Acosta, Enrique Caviedes-Vidal, Seth R Bordenstein
Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and L. ruibali, and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely-related lizard species harbor distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39...
November 15, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27856622/in-vitro-fermentation-of-b-gos-impact-on-faecal-bacterial-populations-and-metabolic-activity-in-autistic-and-non-autistic-children
#10
Roberta Grimaldi, Drinalda Cela, Jonathan R Swann, Jelena Vulevic, Glenn R Gibson, George Tzortzis, Adele Costabile
Children with autism spectrum disorders (ASD) often suffer gastrointestinal problems consistent with imbalances in the gut microbial population. Treatment with antibiotics or pro/prebiotics has been postulated to regulate microbiota and improve gut symptoms, but there is a lack of evidence for such approaches, especially for prebiotics. This study assessed the influence of a prebiotic galactooligosaccharide (B-GOS) on gut microbial ecology and metabolic function using faecal samples from autistic and non-autistic children in an in vitro gut model system...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27836842/microdiversification-of-a-pelagic-polynucleobacter-species-is-mainly-driven-by-acquisition-of-genomic-islands-from-a-partially-interspecific-gene-pool
#11
Matthias Hoetzinger, Johanna Schmidt, Jitka Jezberová, Ulrike Koll, Martin W Hahn
: Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome are clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located...
November 11, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27822539/environmental-disturbances-decrease-the-variability-of-microbial-populations-within-periphyton
#12
Cristina M Herren, Kyle C Webert, Katherine D McMahon
A central pursuit of microbial ecology is to accurately model changes in microbial community composition in response to environmental factors. This goal requires a thorough understanding of the drivers of variability in microbial populations. However, most microbial ecology studies focus on the effects of environmental factors on mean population abundances, rather than on population variability. Here, we imposed several experimental disturbances upon periphyton communities and analyzed the variability of populations within disturbed communities compared with those in undisturbed communities...
May 2016: MSystems
https://www.readbyqxmd.com/read/27814897/characterizing-and-contrasting-the-microbial-ecology-of-laboratory-and-full-scale-ebpr-systems-cultured-on-synthetic-and-real-wastewaters
#13
Erik R Coats, Cynthia K Brinkman, Stephen Lee
The anthropogenic discharge of phosphorus (P) into surface waters can induce the proliferation of cyanobacteria and algae, which can negatively impact water quality. Enhanced biological P removal (EBPR) is an engineered process that can be employed to efficiently remove significant quantities of P from wastewater. Within this engineered system, the mixed microbial consortium (MMC) becomes enriched with polyphosphate accumulating organisms (PAOs). To date much knowledge has been developed on PAOs, and the EBPR process is generally well understood; nonetheless, the engineered process remains underutilized...
January 1, 2017: Water Research
https://www.readbyqxmd.com/read/27811967/differences-in-bacterial-diversity-and-communities-between-glacial-snow-and-glacial-soil-on-the-chongce-ice-cap-west-kunlun-mountains
#14
Guang Li Yang, Shu Gui Hou, Ri Le Baoge, Zhi Guo Li, Hao Xu, Ya Ping Liu, Wen Tao Du, Yong Qin Liu
A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27793217/exercise-and-prebiotics-produce-stress-resistance-converging-impacts-on-stress-protective-and-butyrate-producing-gut-bacteria
#15
A Mika, N Rumian, A B Loughridge, M Fleshner
The gut microbial ecosystem can mediate the negative health impacts of stress on the host. Stressor-induced disruptions in microbial ecology (dysbiosis) can lead to maladaptive health effects, while certain probiotic organisms and their metabolites can protect against these negative impacts. Prebiotic diets and exercise are feasible and cost-effective strategies that can increase stress-protective bacteria and produce resistance against the detrimental behavioral and neurobiological impacts of stress. The goal of this review is to describe research demonstrating that both prebiotic diets and exercise produce adaptations in gut ecology and the brain that arm the organism against inescapable stress-induced learned helplessness...
2016: International Review of Neurobiology
https://www.readbyqxmd.com/read/27790207/transitioning-from-microbiome-composition-to-microbial-community-interactions-the-potential-of-the-metaorganism-hydra-as-an-experimental-model
#16
Peter Deines, Thomas C G Bosch
Animals are home to complex microbial communities, which are shaped through interactions within the community, interactions with the host, and through environmental factors. The advent of high-throughput sequencing methods has led to novel insights in changing patterns of community composition and structure. However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion. The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27770517/microbiological-and-bioinformatics-analysis-of-primary-sjogren-s-syndrome-patients-with-normal-salivation
#17
Huma Siddiqui, Tsute Chen, Ardita Aliko, Piotr M Mydel, Roland Jonsson, Ingar Olsen
BACKGROUND: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present. OBJECTIVE: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation...
2016: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/27768533/cod-and-nitrogen-removal-and-microbial-communities-in-a-novel-waterfall-biofilm-reactor-operated-at-different-cod-tn-ratios
#18
Siyao Wang, Yuewu Pu, Cheng Wei
The aim of this study was to characterize the pollutant removal efficiency and the microbial communities that arose in a newly designed waterfall biofilm reactor (WFBR) at different chemical oxygen demand/total nitrogen (COD/TN) ratios. The reactor was operated continuously for 28 days at different COD/TN ratios, and its efficiency was evaluated. Results showed that as the thickness of the biofilm increased, the structure of the biofilm encouraged anaerobic-aerobic, anoxic-anaerobic, and fully anaerobic conditions in one reactor...
October 21, 2016: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/27762325/performance-and-microbial-ecology-of-a-nitritation-sequencing-batch-reactor-treating-high-strength-ammonia-wastewater
#19
Wenjing Chen, Xiaohu Dai, Dawen Cao, Sha Wang, Xiaona Hu, Wenru Liu, Dianhai Yang
The partial nitrification (PN) performance and the microbial community variations were evaluated in a sequencing batch reactor (SBR) for 172 days, with the stepwise elevation of ammonium concentration. Free ammonia (FA) and low dissolved oxygen inhibition of nitrite-oxidized bacteria (NOB) were used to achieve nitritation in the SBR. During the 172 days operation, the nitrogen loading rate of the SBR was finally raised to 3.6 kg N/m(3)/d corresponding the influent ammonium of 1500 mg/L, with the ammonium removal efficiency and nitrite accumulation rate were 94...
October 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27761636/bacterial-community-radial-spatial-distribution-in-biofilms-along-pipe-wall-in-chlorinated-drinking-water-distribution-system-of-east-china
#20
Jingqing Liu, Hongxing Ren, Xianbei Ye, Wei Wang, Yan Liu, Liping Lou, Dongqing Cheng, Xiaofang He, Xiaoyan Zhou, Shangde Qiu, Liusong Fu, Baolan Hu
Biofilms in the pipe wall may lead to water quality deterioration and biological instability in drinking water distribution systems (DWDSs). In this study, bacterial community radial-spatial distribution in biofilms along the pipe wall in a chlorinated DWDS of East China was investigated. Three pipes of large diameter (300, 600, and 600 mm) were sampled in this DWDS, including a ductile cast iron pipe (DCIP) with pipe age of 11 years and two gray cast iron pipes (GCIP) with pipe ages of 17 and 19 years, and biofilms in the upper, middle, and lower parts of each pipe wall were collected...
October 19, 2016: Applied Microbiology and Biotechnology
keyword
keyword
96143
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"