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"Microbial ecology"

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https://www.readbyqxmd.com/read/29145139/application-and-microbial-ecology-of-psychrotrophs-in-domestic-wastewater-treatment-at-low-temperature
#1
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/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#2
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
#3
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/29135971/build-your-own-soil-exploring-microfluidics-to-create-microbial-habitat-structures
#4
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
#5
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/29133866/gastric-microbiome-of-indian-patients-with-helicobacter-pylori-infection-and-their-interaction-networks
#6
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/29131365/gut-microbiota-and-body-composition-in-anorexia-nervosa-inpatients-in-comparison-to-athletes-overweight-obese-and-normal-weight-controls
#7
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/29129876/-microbial-ecology-along-the-gastrointestinal-tract
#8
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
https://www.readbyqxmd.com/read/29128765/exploring-the-links-between-groundwater-quality-and-bacterial-communities-near-oil-and-gas-extraction-activities
#9
Inês C Santos, Misty S Martin, Michelle L Reyes, Doug D Carlton, Paula Stigler-Granados, Melissa A Valerio, Kristina W Whitworth, Zacariah L Hildenbrand, Kevin A Schug
Bacterial communities in groundwater are very important as they maintain a balanced biogeochemical environment. When subjected to stressful environments, for example, due to anthropogenic contamination, bacterial communities and their dynamics change. Studying the responses of the groundwater microbiome in the face of environmental changes can add to our growing knowledge of microbial ecology, which can be utilized for the development of novel bioremediation strategies. High-throughput and simpler techniques that allow the real-time study of different microbiomes and their dynamics are necessary, especially when examining larger data sets...
November 9, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29125596/contrasting-the-relative-importance-of-species-sorting-and-dispersal-limitation-in-shaping-marine-bacterial-versus-protist-communities
#10
Wenxue Wu, Hsiao-Pei Lu, Akash Sastri, Yi-Chun Yeh, Gwo-Ching Gong, Wen-Chen Chou, Chih-Hao Hsieh
A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29113091/linking-compositional-and-functional-predictions-to-decipher-the-biogeochemical-significance-in-dfaa-turnover-of-abundant-bacterioplankton-lineages-in-the-north-sea
#11
Bernd Wemheuer, Franziska Wemheuer, Dimitri Meier, Sara Billerbeck, Helge-Ansgar Giebel, Meinhard Simon, Christoph Scherber, Rolf Daniel
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun...
November 5, 2017: Microorganisms
https://www.readbyqxmd.com/read/29089134/evaluation-of-different-16s-rrna-gene-v-regions-for-exploring-bacterial-diversity-in-a-eutrophic-freshwater-lake
#12
Junyi Zhang, Xiao Ding, Rui Guan, Congmin Zhu, Chao Xu, Bingchuan Zhu, Hu Zhang, Zhipeng Xiong, Yingang Xue, Jing Tu, Zuhong Lu
Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake...
October 28, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29075322/pulse-electromagnetic-fields-enhance-extracellular-electron-transfer-in-magnetic-bioelectrochemical-systems
#13
Huihui Zhou, Bingfeng Liu, Qisong Wang, Jianmin Sun, Guojun Xie, Nanqi Ren, Zhiyong Jason Ren, Defeng Xing
BACKGROUND: Microbial extracellular electron transfer (EET) is essential in driving the microbial interspecies interaction and redox reactions in bioelectrochemical systems (BESs). Magnetite (Fe3O4) and magnetic fields (MFs) were recently reported to promote microbial EET, but the mechanisms of MFs stimulation of EET and current generation in BESs are not known. This study investigates the behavior of current generation and EET in a state-of-the-art pulse electromagnetic field (PEMF)-assisted magnetic BES (PEMF-MBES), which was equipped with magnetic carbon particle (Fe3O4@N-mC)-coated electrodes...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29071172/biases-during-dna-extraction-affect-bacterial-and-archaeal-community-profile-of-anaerobic-digestion-samples
#14
Ashira Roopnarain, Mashudu Mukhuba, Rasheed Adeleke, Mokhele Moeletsi
The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods...
December 2017: 3 Biotech
https://www.readbyqxmd.com/read/29066578/r-spondin1-expands-paneth-cells-and-prevents-dysbiosis-induced-by-graft-versus-host-disease
#15
Eiko Hayase, Daigo Hashimoto, Kiminori Nakamura, Clara Noizat, Reiki Ogasawara, Shuichiro Takahashi, Hiroyuki Ohigashi, Yuki Yokoi, Rina Sugimoto, Satomi Matsuoka, Takahide Ara, Emi Yokoyama, Tomohiro Yamakawa, Ko Ebata, Takeshi Kondo, Rina Hiramine, Tomoyasu Aizawa, Yoshitoshi Ogura, Tetsuya Hayashi, Hiroshi Mori, Ken Kurokawa, Kazuma Tomizuka, Tokiyoshi Ayabe, Takanori Teshima
The intestinal microbial ecosystem is actively regulated by Paneth cell-derived antimicrobial peptides such as α-defensins. Various disorders, including graft-versus-host disease (GVHD), disrupt Paneth cell functions, resulting in unfavorably altered intestinal microbiota (dysbiosis), which further accelerates the underlying diseases. Current strategies to restore the gut ecosystem are bacteriotherapy such as fecal microbiota transplantation and probiotics, and no physiological approach has been developed so far...
October 24, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29066255/comparative-analysis-of-microbial-sensing-molecules-in-mucosal-tissues-with-aging
#16
O A Gonzalez, S Kirakodu, M J Novak, A J Stromberg, L Orraca, J Gonzalez-Martinez, A Burgos, J L Ebersole
Host-bacterial interactions at mucosal surfaces require recognition of the bacteria by host cells enabling targeted responses to maintain tissue homeostasis. It is now well recognized that an array of host-derived pattern recognition receptors (PRRs), both cell-bound and soluble, are critical to innate immune engagement of microbes via microbial-associated molecular patterns (MAMP). This report describes the use of a nonhuman primate model to evaluate changes in the expression of these sensing molecules related to aging in healthy gingival tissues...
October 16, 2017: Immunobiology
https://www.readbyqxmd.com/read/29064247/in-situ-stimulation-of-thiocyanate-biodegradation-through-phosphate-amendment-in-gold-mine-tailings-water
#17
Mathew P Watts, Han M Gan, Lee Y Peng, Kim-Anh Lê Cao, John W Moreau
Thiocyanate (SCN(-)) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN(-)-contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN(-); however, little is known regarding the potential of native microbes for in situ SCN(-) biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN(-) biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN(-) biodegradation potential...
November 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29058217/data-analysis-for-gut-microbiota-and-health
#18
Xingpeng Jiang, Xiaohua Hu
In recent years, data mining and analysis of high-throughput sequencing of microbiomes and metagenomic data enable researchers to discover biological knowledge by characterizing the composition and variation of species across environmental samples and to accumulate a huge amount of data, making it feasible to infer the complex principle of species interactions. The interactions of microbes in a microbial community play an important role in microbial ecological system. Data mining provides diverse approachs to identify the correlations between disease and microbes and how microbial species coexist and interact in a host-associated or natural environment...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29057500/the-impact-of-rumen-cannulation-on-the-microbial-community-of-goat-rumens-as-measured-using-16s-rrna-high-throughput-sequencing
#19
L Wang, D Wu, T Yan, L Wang
The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high-throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene...
October 22, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/29056457/vibrio-cholerae-combines-individual-and-collective-sensing-to-trigger-biofilm-dispersal
#20
Praveen K Singh, Sabina Bartalomej, Raimo Hartmann, Hannah Jeckel, Lucia Vidakovic, Carey D Nadell, Knut Drescher
Bacteria can generate benefits for themselves and their kin by living in multicellular, matrix-enclosed communities, termed biofilms, which are fundamental to microbial ecology and the impact bacteria have on the environment, infections, and industry [1-6]. The advantages of the biofilm mode of life include increased stress resistance and access to concentrated nutrient sources [3, 7, 8]. However, there are also costs associated with biofilm growth, including the metabolic burden of biofilm matrix production, increased resource competition, and limited mobility inside the community [9-11]...
November 6, 2017: Current Biology: CB
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