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https://www.readbyqxmd.com/read/29054873/the-enigmatic-genome-of-an-obligate-ancient-spiroplasma-symbiont-in-a-hadal-holothurian
#1
Li-Sheng He, Pei-Wei Zhang, Jiao-Mei Huang, Fang-Chao Zhu, Antoine Danchin, Yong Wang
Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their host are unclear. Here, we sequenced the 424-Kbp genome of "Candidatus Spiroplasma holothuricola" that dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana trench (6140m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of Spiroplasma sp. In this organism, the genes responsible for biosynthesis of amino acids, glycolysis and sugar transporters were lost, strongly suggesting endosymbiosis...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054872/transcriptional-activities-of-the-microbial-consortium-living-with-the-marine-nitrogen-fixing-cyanobacterium-trichodesmium-reveal-potential-roles-in-community-level-nitrogen-cycling
#2
Michael D Lee, Eric A Webb, Nathan G Walworth, Fei-Xue Fu, Noelle A Held, Mak A Saito, David A Hutchins
Trichodesmium are globally distributed cyanobacteria whose nitrogen-fixing capabilities fuel primary production in warm, oligotrophic oceans. Like many photoautotrophs, Trichodesmium serve as hosts to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here we utilized metatranscriptomics to examine gene-expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor similar microbial communities to those of natural populations...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054869/estimating-population-turnover-rates-from-relative-quantification-methods-reveals-microbial-dynamics-in-marine-sediment
#3
Richard Kevorkian, Jordan T Bird, Alexander Shumaker, Karen G Lloyd
Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054657/feed-additives-shift-gut-microbiota-and-enrich-antibiotic-resistance-in-swine-gut
#4
Yi Zhao, Jian-Qiang Su, Xin-Li An, Fu-Yi Huang, Christopher Rensing, Kristian Koefoed Brandt, Yong-Guan Zhu
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Antibiotics and metals are widely used as feed additives and could consequently affect ARGs in swine gut. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) based ARG chip and next-generation 16S rRNA gene amplicon sequencing data were analyzed using multiple statistical approaches to profile the antibiotic resistome and investigate its linkages to antibiotics and metals used as feed additives and to the microbial community composition in freshly collected swine manure samples from three large-scale Chinese pig farms...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054632/nitrogen-removal-by-thiosulfate-driven-denitrification-and-plant-uptake-in-enhanced-floating-treatment-wetland
#5
Lei Gao, Weili Zhou, Suqing Wu, Shengbing He, Jungchen Huang, Xu Zhang
This study investigated the potential of thiosulfate-driven autotrophic enhanced floating treatment wetland (AEFTW) in removing nitrogen from the secondary effluent at the relatively short hydraulic retention times and low S/N ratios. Simultaneous autotrophic and heterotrophic denitrification was observed in AEFTW. The peak TN removal rate (15.3gm(-2)d(-1)) exceeded most of the reported floating treatment wetlands. Based on the kinetic model results, low mean temperature coefficient and high k20 verified that the excellent performance in AEFTW diminished the microbial dependence on temperature...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054556/role-of-biochar-as-an-additive-in-organic-waste-composting
#6
REVIEW
M A Sanchez-Monedero, M L Cayuela, A Roig, K Jindo, C Mondini, N Bolan
The use of biochar in organic waste composting has attracted interest in the last decade due to the environmental and agronomical benefits obtained during the process. Biochar presents favourable physicochemical properties, such as large porosity, surface area and high cation exchange capacity, enabling interaction with major nutrient cycles and favouring microbial growth in the composting pile. The enhanced environmental conditions can promote a change in the microbial communities that can affect important microbially mediated biogeochemical cycles: organic matter degradation and humification, nitrification, denitrification and methanogenesis...
September 30, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29053151/highly-structured-prokaryote-communities-exist-within-the-skeleton-of-coral-colonies
#7
Vanessa R Marcelino, Madeleine Jh van Oppen, Heroen Verbruggen
Physiological performance, disease and bleaching prevalence are often patchy within individual coral colonies. These responses are largely influenced by coral-associated microbes, but how the coral microbiome changes over small spatial scales has never been quantified before. We performed a high-resolution quantification of the spatial scale of microbial species turnover (β-diversity) within skeletons of boulder-forming Porites corals. We found very strong prokaryotic species turnover across spatial scales ranging from 4 mm to 2 m within individual colonies, possibly resulting from dispersal limitation and microbial interactions...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29053146/the-plant-circadian-clock-influences-rhizosphere-community-structure-and-function
#8
Charley J Hubbard, Marcus T Brock, Linda Ta van Diepen, Loïs Maignien, Brent E Ewers, Cynthia Weinig
Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29051760/interplay-of-gtpases-and-cytoskeleton-in-cellular-barrier-defects-during-gut-inflammation
#9
REVIEW
Rocío López-Posadas, Michael Stürzl, Imke Atreya, Markus F Neurath, Nathalie Britzen-Laurent
An essential role of the intestine is to build and maintain a barrier preventing the luminal gut microbiota from invading the host. This involves two coordinated physical and immunological barriers formed by single layers of intestinal epithelial and endothelial cells, which avoid the activation of local immune responses or the systemic dissemination of microbial agents, and preserve tissue homeostasis. Accordingly, alterations of epithelial and endothelial barrier functions have been associated with gut inflammation, for example during inflammatory bowel disease (IBD)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29050770/genomic-plasticity-between-human-and-mycobacterial-dna-a-review
#10
REVIEW
Lawal Danjuma, Mok Pooi Ling, Rukman Awang Hamat, Akon Higuchi, Abdullah A Alarfaj, Marlina, Giovanni Benelli, Palanisamy Arulselvan, Mariappan Rajan, Suresh Kumar Subbiah
Mycobacterium tuberculosis has a remarkable ability of long-term persistence despite vigorous host immunity and prolonged therapy. The bacteria persist in secure niches such as the mesenchymal stem cells in the bone marrow and reactivate the disease, leading to therapeutic failure. Many bacterial cells can remain latent within a diseased tissue so that their genetic material can be incorporated into the genetic material of the host tissue. This incorporated genetic material reproduces in a manner similar to that of cellular DNA...
December 2017: Tuberculosis
https://www.readbyqxmd.com/read/29050425/sodium-butyrate-improved-performance-while-modulating-the-cecal-microbiota-and-regulating-the-expression-of-intestinal-immune-related-genes-of-broiler-chickens
#11
C Bortoluzzi, A A Pedroso, J J Mallo, M Puyalto, W K Kim, T J Applegate
This study evaluated the effect of sodium butyrate (SB) on performance, expression of immune-related genes in the cecal tonsils, and cecal microbiota of broiler chickens when dietary energy and amino acids concentrations were reduced. Day-old male Ross 708 broiler chicks were fed dietary treatments in a 3 × 2 factorial design (8 pens per treatment) with 3 dietary formulations (control diet; reduction of 2.3% of amino acids and 60 kcal/kg; and reduction of 4.6% of amino acids and 120 kcal/kg) with or without the inclusion of 0...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29049387/quantifying-the-strength-of-quorum-sensing-crosstalk-within-microbial-communities
#12
Kalinga Pavan T Silva, Prithiviraj Chellamuthu, James Q Boedicker
In multispecies microbial communities, the exchange of signals such as acyl-homoserine lactones (AHL) enables communication within and between species of Gram-negative bacteria. This process, commonly known as quorum sensing, aids in the regulation of genes crucial for the survival of species within heterogeneous populations of microbes. Although signal exchange was studied extensively in well-mixed environments, less is known about the consequences of crosstalk in spatially distributed mixtures of species...
October 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29049360/the-bacterial-virulence-factor-caga-induces-microbial-dysbiosis-that-contributes-to-excessive-epithelial-cell-proliferation-in-the-drosophila-gut
#13
Tiffani Alvey Jones, Diane Z Hernandez, Zoë C Wong, Anica M Wandler, Karen Guillemin
Gut microbiota facilitate many aspects of human health and development, but dysbiotic microbiota can promote hyperplasia and inflammation and contribute to human diseases such as cancer. Human patients infected with the gastric cancer-causing bacterium Helicobacter pylori have altered microbiota; however, whether dysbiosis contributes to disease in this case is unknown. Many H. pylori human disease phenotypes are associated with a potent virulence protein, CagA, which is translocated into host epithelial cells where it alters cell polarity and manipulates host-signaling pathways to promote disease...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29048927/early-origins-of-asthma-role-of-microbial-dysbiosis-and-metabolic-dysfunction
#14
Fernando D Martinez, Stefano Guerra
Asthma is a developmental disease that affects airway growth and is characterized by inappropriate responses to a variety of environmental stimuli. Recent advances point to two altered early life pathways as major determinants of asthma risk. In the "microbial" pathway, pre- and post-natal exposures to microbiota-loaded farm environments block gene-virus interactions (e.g., interactions between risk alleles in chromosome 17q21 and lower respiratory illnesses [LRI] by rhinovirus) that are associated with asthma development...
October 19, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29048537/group-living-and-male-dispersal-predict-the-core-gut-microbiome-in-wild-baboons
#15
Laura E Grieneisen, Josh Livermore, Susan Alberts, Jenny Tung, Elizabeth A Archie
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e...
October 1, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29046664/regulation-structured-dynamic-metabolic-model-provides-a-potential-mechanism-for-delayed-enzyme-response-in-denitrification-process
#16
Hyun-Seob Song, Dennis G Thomas, James C Stegen, Minjing Li, Chongxuan Liu, Xuehang Song, Xingyuan Chen, Jim K Fredrickson, John M Zachara, Timothy D Scheibe
In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community's traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29046636/targeting-the-immune-system-with-plant-lectins-to-combat-microbial-infections
#17
REVIEW
Jannyson J B Jandú, Roberval N Moraes Neto, Adrielle Zagmignan, Eduardo M de Sousa, Maria C A Brelaz-de-Castro, Maria T Dos Santos Correia, Luís C N da Silva
The arsenal of drugs available to treat infections caused by eukaryotic and prokaryotic microbes has been declining exponentially due to antimicrobial resistance phenomenon, leading to an urgent need to develop new therapeutic strategies. Host-directed immunotherapy has been reported as an attractive option to treat microbial infections. It consists in the improvement of host defenses by increasing the expression of inflammatory mediators and/or controlling of inflammation-induced tissue injury. Although the in vitro antimicrobial and immunomodulatory activities of lectins have been extensively demonstrated, few studies have evaluated their in vivo effects on experimental models of infections...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29046620/the-dental-calculus-metabolome-in-modern-and-historic-samples
#18
Irina M Velsko, Katherine A Overmyer, Camilla Speller, Lauren Klaus, Matthew J Collins, Louise Loe, Laurent A F Frantz, Krithivasan Sankaranarayanan, Cecil M Lewis, Juan Bautista Rodriguez Martinez, Eros Chaves, Joshua J Coon, Greger Larson, Christina Warinner
INTRODUCTION: Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29045252/altered-gut-microbiome-composition-in-hiv-infection-causes-effects-and-potential-intervention
#19
Alessandra Bandera, Ilaria De Benedetto, Giorgio Bozzi, Andrea Gori
PURPOSE OF REVIEW: Aim of this review is to summarize the alterations occurring in gut microbiome composition after HIV infection, and to underline how intestinal dysbiosis can affect immune homeostasis, immune recovery, and persisting immune activation under antiretroviral therapy (ART). Many interventions have been suggested, mostly with inconclusive results. RECENT FINDINGS: Recent evidence showed that gut microbiota from HIV-infected patients harbor reproducible differences compared to uninfected individuals...
October 17, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/29043005/impact-of-supplementation-with-a-food-derived-microbial-community-on-obesity-associated-inflammation-and-gut-microbiota-composition
#20
Marianna Roselli, Chiara Devirgiliis, Paola Zinno, Barbara Guantario, Alberto Finamore, Rita Rami, Giuditta Perozzi
BACKGROUND: Obesity is a complex pathology associated with dysbiosis, metabolic alterations, and low-grade chronic inflammation promoted by immune cells, infiltrating and populating the adipose tissue. Probiotic supplementation was suggested to be capable of counteracting obesity-associated immune and microbial alterations, based on its proven immunomodulatory activity and positive effect on gut microbial balance. Traditional fermented foods represent a natural source of live microbes, including environmental strains with probiotic features, which could transiently colonise the gut...
2017: Genes & Nutrition
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