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"Microbial ecology"

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https://www.readbyqxmd.com/read/28453559/evaluation-of-the-reproducibility-of-amplicon-sequencing-with-illumina-miseq-platform
#1
Chongqing Wen, Liyou Wu, Yujia Qin, Joy D Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33...
2017: PloS One
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#2
Konstantin Yarygin, Alexander Tyakht, Andrey Larin, Elena Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions...
2017: PloS One
https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#3
Arghya Mukherjee, Bobby Chettri, James S Langpoklakpam, Pijush Basak, Aravind Prasad, Ashis K Mukherjee, Maitree Bhattacharyya, Arvind K Singh, Dhrubajyoti Chattopadhyay
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28435195/intestinal-microbial-ecology-and-hematological-parameters-of-broiler-fed-cassava-waste-pulp-fermented-with-acremonium-charticola
#4
Sugiharto Sugiharto, Turrini Yudiarti, Isroli Isroli, Endang Widiastuti, Fatan Dwi Putra
AIM: The aim of this study was to evaluate the effect of feeding Acremonium charticola-fermented cassava pulp (AC-FCP) on the intestinal microbial ecology and hematological indices of broiler chickens. MATERIALS AND METHODS: A total of 240 male Lohman day-old-chicks were randomly allotted to one of the four experimental diets including control diet, control diet + antimicrobials (neomycin; 300 mg/kg diet), diet containing AC-FCP (16 g/100 g diet) or diet containing AC-FCP + antimicrobials...
March 2017: Veterinary World
https://www.readbyqxmd.com/read/28430940/unravelling-microbial-ecology-of-industrial-scale-kombucha-fermentations-by-metabarcoding-and-culture-based-methods
#5
M Coton, A Pawtowski, B Taminiau, G Burgaud, F Deniel, L Coulloume-Labarthe, P A Fall, G Daube, E Coton
Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unravelled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, a study compared microbial communities from industrial scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches...
April 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#6
REVIEW
Kenneth Wasmund, Marc Mußmann, Alexander Loy
Almost the entire seafloor is covered with sediments that can be more than 10,000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes...
April 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28419726/chemotaxonomic-characterization-of-the-thaumarchaeal-lipidome
#7
Felix J Elling, Martin Könneke, Graeme W Nicol, Michaela Stieglmeier, Barbara Bayer, Eva Spieck, José R de la Torre, Kevin W Becker, Michael Thomm, James I Prosser, Gerhard J Herndl, Christa Schleper, Kai-Uwe Hinrichs
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidizing thaumarchaeal cultures representing all four characterized phylogenetic clades...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28419666/microbial-ecology-of-mountain-glacier-ecosystems-biodiversity-ecological-connections-and-implications-of-a-warming-climate
#8
REVIEW
Scott Hotaling, Eran Hood, Trinity L Hamilton
Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28416814/ismej-turns-10-tracking-rapid-progress-in-microbial-ecology
#9
George A Kowalchuk, Mark J Bailey
No abstract text is available yet for this article.
May 2017: ISME Journal
https://www.readbyqxmd.com/read/28414441/suppression-of-enteric-bacteria-by-bacteriophages-importance-of-phage-polyvalence-in-the-presence-of-soil-bacteria
#10
Pingfeng Yu, Jacques Mathieu, Yu Yang, Pedro J J Alvarez
Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168)...
April 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28409116/prepare_taxa_charts-py-a-python-program-to-automate-generation-of-publication-ready-taxonomic-pie-chart-images-from-qiime
#11
Vijay Lakhujani, Chandan Badapanda
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28399822/dominant-bacterial-phyla-in-caves-and-their-predicted-functional-roles-in-c-and-n-cycle
#12
Surajit De Mandal, Raghunath Chatterjee, Nachimuthu Senthil Kumar
BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline...
April 11, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28395941/invasion-science-a-horizon-scan-of-emerging-challenges-and-opportunities
#13
REVIEW
Anthony Ricciardi, Tim M Blackburn, James T Carlton, Jaimie T A Dick, Philip E Hulme, Josephine C Iacarella, Jonathan M Jeschke, Andrew M Liebhold, Julie L Lockwood, Hugh J MacIsaac, Petr Pyšek, David M Richardson, Gregory M Ruiz, Daniel Simberloff, William J Sutherland, David A Wardle, David C Aldridge
We identified emerging scientific, technological, and sociopolitical issues likely to affect how biological invasions are studied and managed over the next two decades. Issues were ranked according to their probability of emergence, pervasiveness, potential impact, and novelty. Top-ranked issues include the application of genomic modification tools to control invasions, effects of Arctic globalization on invasion risk in the Northern Hemisphere, commercial use of microbes to facilitate crop production, the emergence of invasive microbial pathogens, and the fate of intercontinental trade agreements...
April 7, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28387771/who-lives-in-a-fungus-the-diversity-origins-and-functions-of-fungal-endobacteria-living-in-mucoromycota
#14
Paola Bonfante, Alessandro Desirò
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related)...
April 7, 2017: ISME Journal
https://www.readbyqxmd.com/read/28382585/when-pasteurian-science-went-to-sea-the-birth-of-marine-microbiology
#15
Antony Adler, Erik Dücker
In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur's discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and whether organic material in the deep sea was subject to decomposition...
April 5, 2017: Journal of the History of Biology
https://www.readbyqxmd.com/read/28379446/50-important-research-questions-in-microbial-ecology
#16
Rachael E Antwis, Sarah M Griffiths, Xavier A Harrison, Paz Aranega-Bou, Andres Arce, Aimee S Bettridge, Francesca L Brailsford, Alexandre de Menezes, Andrew Devaynes, Kristian M Forbes, Ellen L Fry, Ian Goodhead, Erin Haskell, Chloe Heys, Chloe James, Sarah R Johnston, Gillian R Lewis, Zenobia Lewis, Michael C Macey, Alan McCarthy, James E McDonald, Nasmille L Mejia-Florez, David O'Brien, Chloé Orland, Marco Pautasso, William D K Reid, Heather A Robinson, Kenneth Wilson, William J Sutherland
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: Host-Microbiome Interactions; Health and Infectious Diseases; Human Health and Food Security; Microbial Ecology in a Changing World; Environmental Processes; Functional Diversity; and Evolutionary Processes...
April 3, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28367917/genomics-and-metagenomics-in-microbial-ecology-recent-advances-and-challenges
#17
Takashi Narihiro, Yoichi Kamagata
No abstract text is available yet for this article.
2017: Microbes and Environments
https://www.readbyqxmd.com/read/28364728/microbial-ecology-of-fermentative-hydrogen-producing-bioprocesses-useful-insights-for-driving-the-ecosystem-function
#18
Lea Cabrol, Antonella Marone, Estela Tapia-Venegas, Jean-Philippe Steyer, Gonzalo Ruiz-Filippi, Eric Trably
One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service...
March 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28358885/exogenous-lactobacilli-mitigate-microbial-changes-associated-with-grain-fermentation-corn-oats-and-wheat-by-equine-fecal-microflora-ex-vivo
#19
Brittany E Harlow, Laurie M Lawrence, Patricia A Harris, Glen E Aiken, Michael D Flythe
Cereal grains are often included in equine diets. When starch intake exceeds foregut digestion starch will reach the hindgut, impacting microbial ecology. Probiotics (e.g., lactobacilli) are reported to mitigate GI dysbioses in other species. This study was conducted to determine the effect of exogenous lactobacilli on pH and the growth of amylolytic and lactate-utilizing bacteria. Feces were collected from 3 mature geldings fed grass hay with access to pasture. Fecal microbes were harvested by differential centrifugation, washed, and re-suspended in anaerobic media containing ground corn, wheat, or oats at 1...
2017: PloS One
https://www.readbyqxmd.com/read/28348642/metagenomic-analysis-of-a-complex-community-present-in-pond-sediment
#20
Vivek Negi, Rup Lal
The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis...
2017: Journal of Genomics
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