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"Microbial ecology"

Bachar Cheaib, Malo Le Boulch, Pierre-Luc Mercier, Nicolas Derome
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD)...
2018: Frontiers in Microbiology
Dan Luo, Yufei Gao, Youyou Lu, Mingren Qu, Xiaowen Xiong, Lanjiao Xu, Xianghui Zhao, Ke Pan, Kehui Ouyang
To understand the effects of niacin on the ruminal microbial ecology of cattle under high-concentrate diet condition, Illumina MiSeq sequencing technology was used. Three cattle with rumen cannula were used in a 3 × 3 Latin-square design trial. Three diets were fed to these cattle during 3 periods for 3 days, respectively: high-forage diet (HF; forage-to-concentrate ratio = 80:20), high-concentrate diet (HC; forage-to-concentrate ratio = 20:80), and HC supplemented with 800 mg/kg niacin (HCN). Ruminal pH was measured before feeding and every 2 h after initiating feeding...
June 2017: Animal nutrition
Fengge Zhang, Yunqian Huo, Adam B Cobb, Gongwen Luo, Jiqiong Zhou, Gaowen Yang, Gail W T Wilson, Yingjun Zhang
In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses...
2018: Frontiers in Microbiology
Daiane R B Belgini, Virgínia M Siqueira, Douglas M Oliveira, Samantha G Fonseca, Viviane Piccin-Santos, Roberto S Dias, Larissa Quartaroli, Rodrigo S Souza, Ana Paula R Torres, Maíra P Sousa, Cláudio M Silva, Cynthia C Silva, Sérgio O De Paula, Valéria M Oliveira
Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality...
April 13, 2018: Systematic and Applied Microbiology
Ishfaq Nabi Najar, Mingma Thundu Sherpa, Sayak Das, Saurav Das, Nagendra Thakur
Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches...
May 11, 2018: Science of the Total Environment
Dongyang Deng, Jennifer L Weidhaas, Lian-Shin Lin
No abstract text is available yet for this article.
May 8, 2018: Journal of Hazardous Materials
Christopher J Stewart, Thomas A Auchtung, Nadim J Ajami, Kenia Velasquez, Daniel P Smith, Richard De La Garza, Ramiro Salas, Joseph F Petrosino
Background: The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls. Methods: We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls...
2018: PeerJ
Mayra Carla de Freitas Martins, Rosângela de Freitas, Júlio Cesar Deuvaux, Monique Renon Eller, Luís Augusto Nero, Antônio Fernandes de Carvalho
The microbiota from artisanal cheeses produced in the Amazonian region is evaluated. Samples of artisanal cheeses were obtained from markets in Conceição do Araguaia and Redenção (Pará, Brazil) over rainy and dry seasons, and their biodiversity was assessed by culture-dependent and culture-independent methods. Mean counts of lactic acid bacteria (LAB) in cheeses ranged from 7.32 to 8.84 log CFU/g, for both seasons. Members of genera Lactobacillus, Lactococcus, Weissella, Enterococcus, Pediococcus, and Leuconostoc were predominant...
June 2018: Food Research International
Ana P Semedo-Aguiar, Jose B Pereira-Leal, Ricardo B Leite
The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde...
May 5, 2018: Toxins
Elizaveta V Pershina, Ekaterina A Ivanova, Ilia O Korvigo, Evgeny L Chirak, Nurlan H Sergaliev, Evgeny V Abakumov, Nikolai A Provorov, Evgeny E Andronov
The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing...
August 1, 2018: Science of the Total Environment
Irene Franciosa, Valentina Alessandria, Paola Dolci, Kalliopi Rantsiou, Luca Cocolin
Fermented sausages have a long tradition originating from Europe and they constitute a significant part of the Mediterranean diet. This kind of products has a specific microbiota that is typical of the region or area where they are produced. Therefore, in order to protect the traditional aspect of these products, it is essential to understand the microbial ecology during fermentation by studying the dynamic changes that occur and to select autochthonous starter cultures that can be used in the production. In this paper we summarize the state of the art concerning the selection and use of starter cultures and ecology aspects of naturally fermented sausages...
April 25, 2018: International Journal of Food Microbiology
Huan Li, Tongtong Li, Jiapeng Qu
Vector-borne microbes influence pathogen transmission and blood microbiomes, thereby affecting the emergence of infectious diseases. Thus, understanding the relationship between host and vector microbiomes is of importance. In this study, we investigated the bacterial community composition, diversity and assembly of the flea (Rhadinopsylla dahurica vicina), torsalo (Hypoderma curzonial), and the blood and gut of their shared pika host, Ochotona curzoniae. Bartonella, Sphingomonas and Bradyrhizobium were enriched in blood, while Wolbachia and Fusobacterium were more abundant in fleas and torsaloes...
May 2, 2018: FEMS Microbiology Ecology
Jehane Fadlallah, Hela El Kafsi, Delphine Sterlin, Catherine Juste, Christophe Parizot, Karim Dorgham, Gaëlle Autaa, Doriane Gouas, Mathieu Almeida, Patricia Lepage, Nicolas Pons, Emmanuelle Le Chatelier, Florence Levenez, Sean Kennedy, Nathalie Galleron, Jean-Paul Pais de Barros, Marion Malphettes, Lionel Galicier, David Boutboul, Alexis Mathian, Makoto Miyara, Eric Oksenhendler, Zahir Amoura, Joel Doré, Claire Fieschi, S Dusko Ehrlich, Martin Larsen, Guy Gorochov
Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. Metagenomic analysis highlights an expected pathobiont expansion but a less expected depletion in some typically beneficial symbionts...
May 2, 2018: Science Translational Medicine
Andre C Kalil, Uriel Sandkovsky, Diana F Florescu
BACKGROUND: Severe infections are among the most common causes of death in immunocompromised patients admitted to the intensive care unit. The epidemiology, diagnosis, and treatment of these infections has evolved in the last decade. AIMS: We aim to provide a comprehensive review of these severe infections in this population. SOURCES: Review of the literature pertaining to severe infections in critically ill solid organ transplant (SOT) patients...
April 28, 2018: Clinical Microbiology and Infection
Antonio Castellano-Hinojosa, Caterina Armato, Clementina Pozo, Alejandro González-Martínez, Jesús González-López
Waste treatment and the simultaneous production of energy have gained great interest in the world. In the last decades, scientific efforts have focused largely on improving and developing sustainable bioprocess solutions for energy recovery from challenging waste. Anaerobic digestion (AD) has been developed as a low-cost organic waste treatment technology with a simple setup and relatively limited investment and operating costs. Different technologies such as one-stage and two-stage AD have been developed. The viability and performance of these technologies have been extensively reported, showing the supremacy of two-stage AD in terms of overall energy recovery from biomass under different substrates, temperatures, and pH conditions...
April 30, 2018: Applied Microbiology and Biotechnology
Judith N Lezutekong, Anish Nikhanj, Gavin Y Oudit
The main function of the intestinal barrier is to regulate the absorption of nutrients, electrolytes, and water from the lumen into circulation and to prevent the entry of pathogenic microorganisms and toxic luminal substances. To maintain this function, an ideal microbiota balance is required and gut microbiota are critical for the intestinal epithelial barrier dysfunction and for the maintenance of physiological homeostasis. There is a demonstrable link between dysbiosis and intestinal dysfunction and diseases such as diabetes, obesity, and cardiovascular disease...
April 30, 2018: Clinical Science (1979-)
Michael A Ghebre, Pee Hwee Pang, Sarah Diver, Dhananjay Desai, Mona Bafadhel, Koirobi Haldar, Tatiana Kebadze, Suzanne Cohen, Paul Newbold, Laura Rapley, Joanne Woods, Paul Rugman, Ian D Pavord, Sebastian L Johnston, Michael Barer, Richard D May, Christopher E Brightling
BACKGROUND: Exacerbations of asthma and chronic obstructive pulmonary disease (COPD) are heterogeneous. OBJECTIVE: We sought to investigate the sputum cellular, mediator, and microbiome profiles of both asthma and COPD exacerbations. METHODS: Patients with severe asthma or moderate-to-severe COPD were prospectively recruited to a single centre. Sputum mediators were available in 32 asthma and 73 COPD patients assessed at exacerbation. Biologic clusters were determined using factor and cluster analyses on a panel of sputum mediators...
April 27, 2018: Journal of Allergy and Clinical Immunology
Bryan F Staley, Francis L de Los Reyes, Ling Wang, Morton A Barlaz
The decomposition of landfilled refuse proceeds through distinct phases, each defined by varying environmental factors such as volatile fatty acid concentration, pH, and substrate quality. The succession of microbial communities in response to these changing conditions was monitored in a laboratory-scale simulated landfill to minimize measurement difficulties experienced at field scale. 16S rRNA gene sequences retrieved at separate stages of decomposition showed significant succession in both Bacteria and methanogenic Archaea...
April 28, 2018: Applied Microbiology and Biotechnology
Stefano Campanaro, Laura Treu, Panagiotis G Kougias, Gang Luo, Irini Angelidaki
The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome...
April 20, 2018: Water Research
Federica Cardinali, Vesna Milanović, Andrea Osimani, Lucia Aquilanti, Manuela Taccari, Cristiana Garofalo, Serena Polverigiani, Francesca Clementi, Elena Franciosi, Kieran Tuohy, M Lucia Mercuri, M Serena Altissimi, M Naceur Haouet
The present study promotes the valorization of Fabriano-like fermented sausages, which are central-Italy salami with an origin that dates to the early 17th century, for the possible future selection of autochthonous starter cultures to be used with respect to local traditions. To the best of the authors' knowledge, this study represents the first attempt to define the microbial dynamics in Fabriano-like fermented sausage and the effect of nitrates/nitrites and starter cultures on its natural bacterial biota...
April 21, 2018: International Journal of Food Microbiology
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