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https://www.readbyqxmd.com/read/28449283/physiological-responses-of-reared-sea-bream-sparus-aurata-linnaeus-1758-to-an-amyloodinium-ocellatum-outbreak
#1
M Moreira, D Schrama, F Soares, T Wulff, P Pousão-Ferreira, P Rodrigues
Amyloodiniosis represents a major bottleneck for semi-intensive aquaculture production in Southern Europe, causing extremely high mortalities. Amyloodinium ocellatum is a parasitic dinoflagellate that can infest almost all fish, crustacean and bivalves that live within its ecological range. Fish mortalities are usually attributed to anoxia, associated with serious gill hyperplasia, inflammation, haemorrhage and necrosis in heavy infestations; or with osmoregulatory impairment and secondary microbial infections due to severe epithelial damage in mild infestation...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28449237/the-environmental-and-host-associated-bacterial-microbiota-of-arctic-seawater-farmed-atlantic-salmon-with-ulcerative-disorders
#2
C Karlsen, K F Ottem, Øyvind Jakobsen Brevik, M Davey, H Sørum, H C Winther-Larsen
The Norwegian aquaculture of Atlantic salmon (Salmo salar L.) is hampered by ulcerative disorders associated with bacterial infections. Chronic ulceration may provide microenvironments that disturb the normal microbial biodiversity of external surfaces. Studying the composition of microbial communities in skin ulcers will enhance our understanding of ulcer aetiology. To achieve this, we tested marine farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and end of summer (September), in addition to skin mucus of healthy individuals...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28448941/geochemistry-and-microbial-diversity-of-cave-waters-in-the-gypsum-karst-aquifers-of-emilia-romagna-region-italy
#3
Ilenia M D'Angeli, Diana I Serrazanetti, Chiara Montanari, Lucia Vannini, Fausto Gardini, Jo De Waele
Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO4, HCO3, Cl, NO3) and some minor constituents (F, Br, NH4 and PO4), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#4
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/28447935/host-selected-mutations-converging-on-a-global-regulator-drive-an-adaptive-leap-by-bacteria-to-symbiosis
#5
Molly Sabrina Pankey, Randi L Foxall, Ian M Ster, Lauren A Perry, Brian M Schuster, Rachel A Donner, Matthew Coyle, Vaughn S Cooper, Cheryl A Whistler
Host immune and physical barriers protect against pathogens but also impede the establishment of essential symbiotic partnerships. To reveal mechanisms by which beneficial organisms adapt to circumvent host defenses, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri through Euprymna scolopes squid light organs. Serial squid passaging of bacteria produced eight distinct mutations in the binK sensor kinase gene that conferred an exceptional selective advantage demonstrated through both empirical and theoretical analysis...
April 27, 2017: ELife
https://www.readbyqxmd.com/read/28447371/cooperation-in-microbial-communities-and-their-biotechnological-applications
#6
REVIEW
Matteo Cavaliere, Song Feng, Orkun Soyer, Jose I Jimenez
Microbial communities are increasingly utilised in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic crossfeeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins, and analyse their evolutionary resilience...
April 26, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28444190/biological-aging-and-the-human-gut-microbiota
#7
Vincent J Maffei, Sangkyu Kim, Eugene Blanchard, Meng Luo, S Michal Jazwinski, Christopher M Taylor, David A Welsh
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity...
April 25, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28440278/an-insider-s-perspective-bacteroides-as-a-window-into-the-microbiome
#8
REVIEW
Aaron G Wexler, Andrew L Goodman
Over the last decade, our appreciation for the contribution of resident gut microorganisms-the gut microbiota-to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium...
April 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#9
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/28439034/teleosts-as-model-organisms-to-understand-host-microbe-interactions
#10
Emily A Lescak, Kathryn C Milligan-Myhre
Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns whether observations in artificial conditions are actually reflective of what occurs in the wild...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28437661/ecological-patterns-of-seed-microbiome-diversity-transmission-and-assembly
#11
REVIEW
Ashley Shade, Marie-Agnès Jacques, Matthieu Barret
Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed...
April 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28437572/nearly-a-decade-long-repeatable-seasonal-diversity-patterns-of-bacterioplankton-communities-in-the-eutrophic-lake-donghu-wuhan-china
#12
Qingyun Yan, James C Stegen, Yuhe Yu, Ye Deng, Xinghao Li, Shu Wu, LilI Dai, Xiang Zhang, Jinjin Li, Chun Wang, Jiajia Ni, Xuemei Li, Hongjuan Hu, Fanshu Xiao, Weisong Feng, Daliang Ning, Zhili H E, Joy D Van Nostrand, Liyou Wu, Jizhong Zhou
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28435195/intestinal-microbial-ecology-and-hematological-parameters-of-broiler-fed-cassava-waste-pulp-fermented-with-acremonium-charticola
#13
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
#14
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/28429833/the-microbially-mediated-soil-organic-carbon-loss-under-degenerative-succession-in-an-alpine-meadow
#15
Yuguang Zhang, Xiao Liu, Jing Cong, Hui Lu, Yuyu Sheng, Xiulei Wang, Diqiang Li, Xueduan Liu, Huaqun Yin, Jizhong Zhou, Ye Deng
Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially-mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analyzed using high-throughput technologies, including Illumina sequencing and GeoChip functional gene arrays. The soil microbial community structure and diversity were significantly (P < 0...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#16
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
#17
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
#18
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/28418713/defence-factors-of-vaginal-lactobacilli
#19
S Kovachev
Accurate knowledge of the composition and ecology of the vaginal microbial environment in healthy women is necessary for understanding lactobacilli-dominated normal microbiota and the mechanisms by which it reduces disease risk. The vagina and its microbiota form a balanced ecosystem; any movement outside the normal range for this ecosystem of obligate and/or facultative microbes, termed dysbacteriosis, can lead to infection and disease. This review summarizes recent research on the vaginal ecosystem, the Lactobacillus species that dominate it, and the means by which they suppress the growth, development, and/or proliferation of pathogenic microbial species...
April 18, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28418070/a-signature-of-tree-health-shifts-in-the-microbiome-and-the-ecological-drivers-of-horse-chestnut-bleeding-canker-disease
#20
Britt Koskella, Sean Meaden, William J Crowther, Roosa Leimu, C Jessica E Metcalf
Host susceptibility to pathogens can be shaped by genetic, ecological, and evolutionary factors. The ability to predict the spread of disease therefore requires an integrated understanding of these factors, including effects of pests on pathogen growth and competition between pathogens and commensal microbiota for host resources. We examined interactions between the leaf-mining moth Cameraria ohridella, the bacterial causal agent of bleeding canker disease Pseudomonas syringae pv aesculi, and the bark-associated microbiota of horse chestnut (Aesculus hippocastanum) trees...
April 18, 2017: New Phytologist
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