keyword
MENU ▼
Read by QxMD icon Read
search

microbial ecology

keyword
https://www.readbyqxmd.com/read/29147568/environmental-influences-on-the-skin-microbiome-of-humans-and-cattle-in-rural-madagascar
#1
Melissa B Manus, James J Yu, Lawrence P Park, Olaf Mueller, Sarah C Windsor, Julie E Horvath, Charles L Nunn
Background and objectives: The skin harbors a dynamic community of microorganisms, where contact with humans, other animals and the environment can alter microbial communities. Most research on the human skin microbiome features Western populations living in hygienic conditions, yet these populations have vastly different patterns of environmental contact than the majority of people on Earth, including those living in developing countries. Methodology: We studied skin microbial communities of humans and cattle (zebu) in rural Madagascar to investigate how zebu ownership affects microbial composition of the human skin, and to characterize non-Western human and zebu skin communities more generally...
2017: Evolution, Medicine, and Public Health
https://www.readbyqxmd.com/read/29146901/genome-driven-evolutionary-game-theory-helps-understand-the-rise-of-metabolic-interdependencies-in-microbial-communities
#2
Ali R Zomorrodi, Daniel Segrè
Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146250/revitalization-of-plant-growth-promoting-rhizobacteria-for-sustainable-development-in-agriculture
#3
REVIEW
Sushanto Gouda, Rout George Kerry, Gitishree Das, Spiros Paramithiotis, Han-Seung Shin, Jayanta Kumar Patra
The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29146247/distribution-of-apple-and-blackcurrant-microbiota-in-lithuania-and-the-czech-republic
#4
Iglė Vepštaitė-Monstavičė, Juliana Lukša, Ramunė Stanevičienė, Živilė Strazdaitė-Žielienė, Vyacheslav Yurchenko, Saulius Serva, Elena Servienė
The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#5
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29145139/application-and-microbial-ecology-of-psychrotrophs-in-domestic-wastewater-treatment-at-low-temperature
#6
Zhenzhen Xu, Yue Ben, Zhonglin Chen, Anxi Jiang, Jimin Shen, Xiaoyun Han
The feasibility of a bunch of screened psychrotrophs being applied to low-temperature wastewater treatment was investigated. The screened psychrophillic strains are capable of growth at a broad temperature-range from 0 to 40 °C and exhibit a preferable TTC-dehydrogenase activity at low temperature (4-10 °C). Along the sharply fluctuant temperatures (25-4-25 °C), the screened psychrotrophs (compared with the indigenous mesophiles) demonstrate less fluctuations of COD removal and more rapid recovery after temperature shocks...
October 24, 2017: Chemosphere
https://www.readbyqxmd.com/read/29145121/role-of-acid-alkali-treatment-in-primary-sludge-anaerobic-fermentation-insights-into-microbial-community-structure-functional-shifts-and-metabolic-output-by-high-throughput-sequencing
#7
Xiao Huang, Wenyi Dong, Hongjie Wang, Yangyang Feng
This study aimed to investigate the effect of acid- or alkali-treatment on volatile fatty acids (VFAs) production and microbiological mechanism during primary sludge anaerobic fermentation. Seven fermentation experiments were conducted at different pH (3-12). Results showed that the optimal pH was 10 for accumulation of VFAs. High-throughput sequencing results indicated that acid and alkali treatment could inhibit Erysipelotrichaceae_UCG-004 and norank_p_Aminicenantes, instead of promoting Pseudomonas and Tissierella at acidic and alkaline condition, respectively...
November 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29143489/spatial-variation-in-the-parasite-communities-and-genomic-structure-of-urban-rats-in-new-york-city
#8
L P Angley, M Combs, C Firth, M J Frye, I Lipkin, J L Richardson, J Munshi-South
Brown rats (Rattus norvegicus) are a globally distributed pest. Urban habitats can support large infestations of rats, posing a potential risk to public health from the parasites and pathogens they carry. Despite the potential influence of rodent-borne zoonotic diseases on human health, it is unclear how urban habitats affect the structure and transmission dynamics of ectoparasite and microbial communities (all referred to as "parasites" hereafter) among rat colonies. In this study, we use ecological data on parasites and genomic sequencing of their rat hosts to examine associations between spatial proximity, genetic relatedness and the parasite communities associated with 133 rats at five sites in sections of New York City with persistent rat infestations...
November 16, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#9
Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29140977/low-cost-and-open-source-multi-fluorescence-imaging-system-for-teaching-and-research-in-biology-and-bioengineering
#10
Isaac Nuñez, Tamara Matute, Roberto Herrera, Juan Keymer, Timothy Marzullo, Timothy Rudge, Fernán Federici
The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates...
2017: PloS One
https://www.readbyqxmd.com/read/29138307/microdiversity-of-an-abundant-terrestrial-bacterium-encompasses-extensive-variation-in-ecologically-relevant-traits
#11
Alexander B Chase, Ulas Karaoz, Eoin L Brodie, Zulema Gomez-Lunar, Adam C Martiny, Jennifer B H Martiny
Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29135971/build-your-own-soil-exploring-microfluidics-to-create-microbial-habitat-structures
#12
Kristin Aleklett, E Toby Kiers, Pelle Ohlsson, Thomas S Shimizu, Victor Ea Caldas, Edith C Hammer
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.The ISME Journal advance online publication, 14 November 2017; doi:10.1038/ismej.2017.184.
November 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/29134738/fungal-community-reveals-less-dispersal-limitation-and-potentially-more-connected-network-than-that-of-bacteria-in-bamboo-forest-soils
#13
Xian Xiao, Yuting Liang, Sai Zhou, Shunyao Zhuang, Bo Sun
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134586/iron-chloride-flocculation-of-bacteriophages-from-seawater
#14
Bonnie T Poulos, Seth G John, Matthew B Sullivan
Viruses influence ecosystem dynamics by modulating microbial host population dynamics, evolutionary trajectories and metabolic outputs. While they are ecologically important across diverse ecosystems, viruses are challenging to study due to minimal biomass often obtained when sampling natural communities. Here we describe a technique using chemical flocculation, filtration and resuspension to recover bacteriophages from seawater and other natural waters. The method uses iron to precipitate viruses which are recovered by filtration onto large-pore size membranes and then resuspended using a buffer containing magnesium and a reductant (ascorbic acid or oxalic acid) at slightly acid pH (6-6...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29133866/gastric-microbiome-of-indian-patients-with-helicobacter-pylori-infection-and-their-interaction-networks
#15
Anubhav Das, Verima Pereira, Shruti Saxena, Tarini Shankar Ghosh, D Anbumani, Satyabrata Bag, Bhabatosh Das, G Balakrish Nair, Philip Abraham, Sharmila S Mande
The gastric microbiome is suspected to have a role in the causation of diseases by Helicobacter pylori. Reports on their relative abundance vis-à-vis H. pylori are available from various ethnic and geographic groups, but little is known about their interaction patterns. Endoscopic mucosal biopsy samples from the gastric antrum and corpus of 39 patients with suspected H. pylori infection were collected and microbiomes were analyzed by 16S rDNA profiling. Four groups of samples were identified, which harbored Helicobacter as well as a diverse group of bacteria including Lactobacillus, Halomonas and Prevotella...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133838/fungal-networks-serve-as-novel-ecological-routes-for-enrichment-and-dissemination-of-antibiotic-resistance-genes-as-exhibited-by-microcosm-experiments
#16
Rashid Nazir, Ju-Pei Shen, Jun-Tao Wang, Hang-Wei Hu, Ji-Zheng He
Antibiotic resistance genes (ARGs) in the environment and their subsequent acquisition by clinically important microorganisms are a serious concern. However, the spread of environmental ARGs remain largely unknown. We report, for the first time, the involvement of soil fungi in the distribution of bacteria with ARGs via soil microcosms. qPCR assay detected unique ARGs specifically found in the mycosphere of different fungi. Interestingly, the taxonomically and ecologically different fungi exerted different selection pressures on ARGs originating from the same source...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29131839/diversity-and-feeding-strategies-of-soil-microfauna-along-elevation-gradients-in-himalayan-cold-deserts
#17
Miloslav Devetter, Ladislav Háněl, Klára Řeháková, Jiří Doležal
High-elevation cold deserts in Tibet and Himalaya are one of the most extreme environments. One consequence is that the diversity of macrofauna in this environment is often limited, and soil microorganisms have a more influential role in governing key surface and subsurface bioprocesses. High-elevation soil microfauna represent important components of cold ecosystems and dominant consumers of microbial communities. Still little is known about their diversity and distribution on the edge of their reproductive and metabolic abilities...
2017: PloS One
https://www.readbyqxmd.com/read/29131365/gut-microbiota-and-body-composition-in-anorexia-nervosa-inpatients-in-comparison-to-athletes-overweight-obese-and-normal-weight-controls
#18
Sabrina Mörkl, Sonja Lackner, Wolfram Müller, Gregor Gorkiewicz, Karl Kashofer, Andreas Oberascher, Annamaria Painold, Anna Holl, Peter Holzer, Andreas Meinitzer, Harald Mangge, Sandra Holasek
OBJECTIVES: Anorexia nervosa (AN) is a heterogeneous eating disorder associated with alterations of body structure and the gut microbiome. We aimed to investigate the gut microbiota composition of a large female cohort including different BMI groups and activity levels along with body composition parameters. METHOD: 106 female participants were included in this cross-sectional study: AN patients (n = 18), athletes (n = 20), normal weight (n = 26), overweight (n = 22), and obese women (n = 20)...
November 13, 2017: International Journal of Eating Disorders
https://www.readbyqxmd.com/read/29130182/a-culture-dependent-method-for-the-identification-of-quorum-quenching-enzymes-of-microbial-origin
#19
Kaihao Tang, Xiao-Hua Zhang
Although it has been more than a decade since the first discovery of AHL lactonase AiiA in Bacillus sp. 240B1, we are only beginning to understand the diversity of quorum quenching (QQ) enzymes. Most of the previously identified QQ enzymes are derived from nonmarine microorganisms. A novel marine-derived secretory AHL lactonase, MomL, was found in Muricauda olearia in our previous work and represents a novel type of AHL lactonase widespread in the ocean. Herein, we describe a culture-dependent method for the identification of microbial QQ enzymes, especially the high-throughput method for screening QQ bacteria from cultivable bacterial strains...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129876/-microbial-ecology-along-the-gastrointestinal-tract
#20
Ethan T Hillman, Hang Lu, Tianming Yao, Cindy H Nakatsu
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem...
November 10, 2017: Microbes and Environments
keyword
keyword
87074
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"