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microbial ecology

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https://www.readbyqxmd.com/read/28339946/pasture-flock-chicken-cecal-microbiome-responses-to-prebiotics-and-plum-fiber-feed-amendments
#1
S H Park, A Perrotta, I Hanning, S Diaz-Sanchez, S Pendleton, E Alm, S C Ricke
When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives...
March 3, 2017: Poultry Science
https://www.readbyqxmd.com/read/28337900/the-fingerprint-of-the-human-gastrointestinal-tract-microbiota-a-hypothesis-of-molecular-mapping
#2
G Tomasello, M Mazzola, A Jurjus, F Cappello, F Carini, P Damiani, A Gerges Geagea, M N Zeenny, A Leone
The precise etiology of Inflammatory Bowel Disease (IDB) remains unclear and several factors are believed to play a role in its development and progression, including the composition of microbial communities resident in the gastrointestinal tract. Human intestinal microbiota are extensive with at least 15,000-36,000 bacterial species. However, thanks to the new development in sequencing and molecular taxonomic methodologies, our understanding of the microbiota population composition, dynamics, and ecology has greatly increased...
January 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28335309/separation-of-bacteria-protozoa-and-carbon-nanotubes-by-density-gradient-centrifugation
#3
Monika Mortimer, Elijah J Petersen, Bruce A Buchholz, Patricia A Holden
Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates...
October 12, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334408/leaf-endophytic-fungus-interacts-with-precipitation-to-alter-belowground-microbial-communities-in-primary-successional-dunes
#4
Lukas Bell-Dereske, Cristina Takacs-Vesbach, Stephanie N Kivlin, Sarah M Emery, Jennifer A Rudgers
Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multi-year field experiment (2010-2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community...
March 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334326/allelopathy-mediated-competition-in-microbial-mats-from-antarctic-lakes
#5
Marc Slattery, Michael P Lesser
Microbial mats are vertically stratified communities that host a complex consortium of microorganisms, dominated by cyanobacteria, that compete for available nutrients and environmental niches, within these extreme habitats. The Antarctic Dry Valleys near McMurdo Sound include a series of lakes within the drainage basin that are bisected by glacial traverses. These lakes are traditionally independent, but recent increases in glacial melting have allowed two lakes (Chad and Hoare) to become connected by a meltwater stream...
February 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334218/reconciliation-between-operational-taxonomic-units-and-species-boundaries
#6
Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek-Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for a bacterial species. Our results show that the robustness of such a generalized cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene...
March 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334205/tetrahymena-phagocytic-vesicles-as-ecological-micro-niches-of-phage-transfer
#7
Iqbal Aijaz, Gerald B Koudelka
The microbial communities in natural environments such as soil, pond water, or animal rumens are comprised of a diverse mixture of bacteria and protozoa including ciliates or flagellates. In such microbiomes, a major source of bacterial mortality is grazing by phagocytic protists. Many protists are omnivorous heterotrophs, feeding on a range of different bacterial species. Due to this indiscriminate feeding, different bacterial species can assemble together in the same phagocytic vesicles where can they potentially exchange genetic material...
March 3, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334191/tu-et-al-microbial-diversity-in-chinese-temperate-steppe-unveiling-the-most-influential-environmental-drivers
#8
Bo Tu, Xavier Domene, Minjie Yao, Chaonan Li, Shiheng Zhang, Yongping Kou, Yansu Wang, Xiangzhen Li
Temperate steppe is extremely sensitive to the current global changes. However, what are the main environmental variables driving microbial diversity in temperate steppe are still unclear, something that impairs doing predictions about the expected effects of global changes on microbe-mediated ecological functions. This is why, in this study, the relationship between soil microbial diversity and environmental variables in Chinese temperate steppe is investigated. In this study, significant correlations between soil bacterial α-diversity and mean annual precipitation (MAP) and the aridity index (AI) were observed at the whole region scale...
March 7, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334109/comparison-of-biofilm-ecology-supporting-growth-of-individual-naegleria-species-in-a-drinking-water-distribution-system
#9
Geoffrey J Puzon, Jason T Wylie, Tom Walsh, Kalan Braun, Matthew J Morgan
Free-living amoebae (FLA) are common components of microbial communities in drinking water distribution systems (DWDS). FLA are of clinical importance both as pathogens and as reservoirs for bacterial pathogens, so identifying the conditions promoting amoebae colonisation of DWDSs is an important public health concern for water utilities. We used high-throughput amplicon sequencing to compare eukaryotic and bacterial communities associated with DWDS biofilms supporting distinct FLA species (N. fowleri, N. lovaniensis or Vermamoeba sp...
February 21, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28330250/deciphering-the-evolutionary-affiliations-among-bacterial-strains-pseudomonas-and-frankia-sp-inhabiting-same-ecological-niche-using-virtual-rflp-and-simulation-based-approaches
#10
Meenakshi Srivastava, Manish Singh Kaushik, Amrita Srivastava, Anumeha Singh, Ekta Verma, Arun Kumar Mishra
To decipher an evolutionary lineage between two different but important bacterial groups, i.e., Pseudomonas strain (γ-Proteobacteria) and Frankia strain (actinobacteria) growing in the same ecological niche in and around of an actinorhizal plant Hippophae salicifolia D. Don, genetic diversity and comparative molecular phylogeny have been investigated using 16S rRNA gene sequences and computer-simulated and virtually directed restriction fragment length polymorphism (RFLP) through 10 restriction enzymes. Bayesian and coalescent analyses on the basis of 16S rRNA gene sequences suggested three major groups with close proximity between Pseudomonas and Frankia isolates...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330235/antimicrobial-activities-of-a-promising-glycolipid-biosurfactant-from-a-novel-marine-staphylococcus-saprophyticus-sbps-15
#11
P Mani, G Dineshkumar, T Jayaseelan, K Deepalakshmi, C Ganesh Kumar, S Senthil Balan
Biosurfactants have gained a renewed interest in the recent years for their commercial application in diverse research areas. Recent evidences suggest that the antimicrobial activities exhibited by biosurfactants make them promising molecules for the application in the field of therapeutics. Marine microbes are well known for their unique metabolic and functional properties; however, few reports are available till date regarding their biosurfactant production and antimicrobial potential. In an ongoing survey for bioactive microbial metabolites from microbes isolated from diverse ecological niches, a marine Staphylococcus saprophyticus SBPS 15 isolated from the petroleum hydrocarbon contaminated coastal site, Puducherry, India, was identified as a promising biosurfactant producer based on multiple screening methods...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330123/microbial-degradation-of-low-density-polyethylene-ldpe-by-aspergillus-clavatus-strain-jask1-isolated-from-landfill-soil
#12
Anudurga Gajendiran, Sharmila Krishnamoorthy, Jayanthi Abraham
Polythene and plastic waste are found to accumulate in the environment, posing a major ecological threat. They are found to be considered non-degradable, once it enters the environment it has been found to remain there indefinitely. However, significant attention has been placed on biodegradable polymer, identification of microbes with degradative potential on plastic material. The aim of the present investigation was to biodegrade low-density polyethylene (LDPE) using potential fungi isolated from landfill soil...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328192/molecular-insights-on-dissolved-organic-matter-transformation-by-supraglacial-microbial-communities
#13
Runa Antony, Amanda S Willoughby, Amanda M Grannas, Victoria Catanzano, Rachel L Sleighter, Meloth Thamban, Patrick G Hatcher, Shanta Nair
Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bio-available and is transformed by resident microbial communities through parallel processes of degradation and synthesis...
March 22, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28323280/defining-the-functional-traits-that-drive-bacterial-decomposer-community-productivity
#14
Rachael Evans, Anna M Alessi, Susannah Bird, Simon J McQueen-Mason, Neil C Bruce, Michael A Brockhurst
Microbial communities are essential to a wide range of ecologically and industrially important processes. To control or predict how these communities function, we require a better understanding of the factors which influence microbial community productivity. Here, we combine functional resource use assays with a biodiversity-ecosystem functioning (BEF) experiment to determine whether the functional traits of constituent species can be used to predict community productivity. We quantified the abilities of 12 bacterial species to metabolise components of lignocellulose and then assembled these species into communities of varying diversity and composition to measure their productivity growing on lignocellulose, a complex natural substrate...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323277/an-alternative-polysaccharide-uptake-mechanism-of-marine-bacteria
#15
Greta Reintjes, Carol Arnosti, Bernhard M Fuchs, Rudolf Amann
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS)...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28320772/mechanism-for-microbial-population-collapse-in-a-fluctuating-resource-environment
#16
Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman-Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts...
March 20, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28319653/the-ecology-of-human-microbiota-dynamics-and-diversity-in-health-and-disease
#17
Antti Karkman, Jenni Lehtimäki, Lasse Ruokolainen
Social welfare, better health care, and urbanization have greatly improved human health and well-being. On the other hand, Western societies suffer from the downsides of the elevated standard of living. Among other factors, the Western diet (poor in dietary fiber), lack of contact with natural biodiversity, and excessive antibiotic use are known to be associated with the increase in chronic inflammatory disorders. Limited exposure to microbial biodiversity, in combination with severe lifestyle-related disturbances to commensal microbial communities, especially during early life, is changing the diversity and composition of human microbiota...
March 20, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28318400/new-frontiers-in-fibers-innovative-and-emerging-research-on-the-gut-microbiome-and-bone-health
#18
Taylor C Wallace, Massimo Marzorati, Lisa Spence, Connie M Weaver, Patricia S Williamson
The complex interactions between the diet, gut microbiome, and host characteristics that provide a functional benefit to the host are an area of great interest and current exploration in the nutrition and health science community. New technologies are available to assess mechanisms that may explain these functional benefits to the host. One emerging functional benefit from changes in the gut microbiome is increased calcium absorption, increased calcium retention, and improved indices of bone health. Prebiotic fibers enhance microbial fermentation in the gut, providing an ecological advantage to specific nonpathogenic bacteria that have the ability to modify an individual's metabolic potential...
March 20, 2017: Journal of the American College of Nutrition
https://www.readbyqxmd.com/read/28317363/-periodontal-inflammation-affects-the-mechanical-and-immune-barrier-functions-of-mice-gut
#19
Xie Meilian, Yu Ting, Zhuo Ying, Huang Xin, Xie Baoyi, Xuan Dongying, Zhang Jincai
OBJECTIVE: To explore the effects of periodontal inflammation on the functions of gut barrier (ecological barrier, mechanical barrier, and immune barrier) in mice. METHODS: Twenty male C57BL/6J mice were randomly divided into perio-dontitis (P) or control (C) groups. The P group was subjected under a 10-day ligation with Porphyromonas gingivalis to induce periodontitis, whereas the C group was ligated with sham. Maxillae were obtained to assess alveolar bone loss...
August 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28317324/big-in-the-benthos-future-change-of-seafloor-community-biomass-in-a-global-body-size-resolved-model
#20
Andrew Yool, Adrian P Martin, Thomas R Anderson, Brian J Bett, Daniel O B Jones, Henry A Ruhl
Deep-water benthic communities in the ocean are almost wholly dependent on near-surface pelagic ecosystems for their supply of energy and material resources. Primary production in sunlit surface waters is channelled through complex food webs that extensively recycle organic material, but lose a fraction as particulate organic carbon (POC) that sinks into the ocean interior. This exported production is further rarefied by microbial breakdown in the abyssal ocean, but a residual ultimately drives diverse assemblages of seafloor heterotrophs...
March 19, 2017: Global Change Biology
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