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MicrobiologyOpen

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https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#1
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217917/a-comprehensive-phylogenetic-analysis-of-copper-transporting-p1b-atpases-from-bacteria-of-the-rhizobiales-order-uncovers-multiplicity-diversity-and-novel-taxonomic-subtypes
#2
Ciro Cubillas, Fabiola Miranda-Sánchez, Antonio González-Sánchez, José Pedro Elizalde, Pablo Vinuesa, Susana Brom, Alejandro García-de Los Santos
The ubiquitous cytoplasmic membrane copper transporting P1B-1 and P1B-3 -type ATPases pump out Cu(+) and Cu(2+) , respectively, to prevent cytoplasmic accumulation and avoid toxicity. The presence of five copies of Cu-ATPases in the symbiotic nitrogen-fixing bacteria Sinorhizobium meliloti is remarkable; it is the largest number of Cu(+) -transporters in a bacterial genome reported to date. Since the prevalence of multiple Cu-ATPases in members of the Rhizobiales order is unknown, we performed an in silico analysis to understand the occurrence, diversity and evolution of Cu(+) -ATPases in members of the Rhizobiales order...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#3
Sylwia Zielińska, Piotr Radkowski, Aleksandra Blendowska, Agnieszka Ludwig-Gałęzowska, Joanna M Łoś, Marcin Łoś
Metagenomics approaches and recent improvements in the next-generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28215046/genome-resolved-metagenomics-of-a-bioremediation-system-for-degradation-of-thiocyanate-in-mine-water-containing-suspended-solid-tailings
#4
Sumayah F Rahman, Rose S Kantor, Robert Huddy, Brian C Thomas, Andries W van Zyl, Susan T L Harrison, Jillian F Banfield
Thiocyanate (SCN(-) ) is a toxic compound that forms when cyanide (CN(-) ), used to recover gold, reacts with sulfur species. SCN(-) -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids...
February 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28213899/human-influence-and-biotic-homogenization-drive-the-distribution-of-escherichia-coli-virulence-genes-in-natural-habitats
#5
Adriana Cabal, Joaquin Vicente, Julio Alvarez, Jose Angel Barasona, Mariana Boadella, Lucas Dominguez, Christian Gortazar
Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E...
February 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28173636/identification-and-characterization-of-a-novel-fusobacterium-nucleatum-adhesin-involved-in-physical-interaction-and-biofilm-formation-with-streptococcus-gordonii
#6
Bruno P Lima, Wenyuan Shi, Renate Lux
To successfully colonize the oral cavity, bacteria must directly or indirectly adhere to available oral surfaces. Fusobacterium nucleatum plays an important role in oral biofilm community development due to its broad adherence abilities, serving as a bridge between members of the oral biofilm that cannot directly bind to each other. In our efforts to characterize the molecular mechanisms utilized by F. nucleatum to physically bind to key members of the oral community, we investigated the involvement of F. nucleatum outer membrane proteins in its ability to bind to the pioneer biofilm colonizer, Streptococcus gordonii...
February 7, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28173613/illumina-sequencing-based-analysis-of-sediment-bacteria-community-in-different-trophic-status-freshwater-lakes
#7
Yu Wan, Xiaohong Ruan, Yaping Zhang, Rongfu Li
Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution...
February 7, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28133926/n-acylhomoserine-lactone-regulation-of-genes-mediating-motility-and-pathogenicity-in-pseudomonas-syringae-pathovar-tabaci-11528
#8
Feifei Cheng, Anzhou Ma, Jinxue Luo, Xuliang Zhuang, Guoqiang Zhuang
Pseudomonas syringae pathovar tabaci 11528 (P. syringae 11528) is a phytopathogen that causes wild-fire disease in soybean and tobacco plants. It utilizes a cell density-dependent regulation system known as quorum sensing (QS). In its QS system, the psyI is responsible for the biosynthesis of N-acylhomoserine lactones (AHLs). By comparing the transcripts from P. syringae 11528 wild-type strain with those of the ΔpsyI mutant using RNA sequencing (RNA-seq) technology, 1118 AHL-regulated genes were identified in the transition from exponential to stationary growth phase...
January 29, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28127946/ribose-operon-repressor-rbsr-contributes-to-the-adhesion-of-aeromonas-hydrophila-to-anguilla-japonica-mucus
#9
Guifang Lin, Wenbo Chen, Yongquan Su, Yingxue Qin, Lixing Huang, Qingpi Yan
The characterization of adhesion between pathogenic bacteria and the host is critical. Pathogenic Aeromonas hydrophila was shown to adhere in vitro to the mucus of Anguilla japonica. To further investigate the adhesion mechanisms of A. hydrophila, a mini-Tn10 transposon mutagenesis system was used to generate an insertion mutant library by cell conjugation. Seven mutants that were impaired in adhesion to mucus were selected out of 332 individual colonies, and mutant M196 was the most severely impaired strain...
January 27, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28127902/the-gut-microbiome-of-hooded-cranes-grus-monacha-wintering-at-shengjin-lake-china
#10
Guanghong Zhao, Lizhi Zhou, Yuanqiu Dong, Yuanyuan Cheng, Yunwei Song
Gut microbes of animals play critical roles in processes such as digestion and immunity. Therefore, identifying gut microbes will shed light on understanding the annual life of animal species, particularly those that are threatened or endangered. In the present study, we conducted nucleotide sequence analyses of the 16S rRNA genes of gut microbiome of the hooded cranes (Grus monacha) wintering at Shengjin Lake, China, by Illumina high-throughput sequencing technology. We acquired 503,398 high-quality sequences and 785 operational taxonomic units (OTUs) from 15 fecal samples from different cranes, representing 22 phyla that were dominated by Firmicutes, Proteobacteria, and Actinobacteria...
January 26, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28127899/transcriptional-and-posttranscriptional-regulation-of-shigella-shut-in-response-to-host-associated-iron-availability-and-temperature
#11
Yahan Wei, Andrew B Kouse, Erin R Murphy
Like most bacteria, Shigella must maintain a precise balance between the necessity and toxicity of iron; a balance that is achieved, at least in part, by regulating the production of bacterial iron acquisition systems in response to specific environmental signals. Using the Shigella heme utilization (Shu) system, S. dysenteriae is able to acquire iron from heme, a potentially rich source of nutritional iron within the otherwise iron-limited environment of the human host. Investigations presented within reveal two distinct molecular mechanisms underlying previously uncharacterized transcriptional and translational regulation of shuT, a gene encoding the periplasmic-binding component of the Shu system...
January 26, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28127894/identification-and-bioactive-potential-of-marine-microorganisms-from-selected-florida-coastal-areas
#12
Anna Christensen, Glenroy D A Martin
The ocean, with its rich untapped chemical biodiversity, continues to serve as a source of potentially new therapeutic agents. The evaluation of the diversity of cultivable microorganisms from the marine sponge Halichondria panicea and ocean sediment samples were examined and their potential as sources of antimicrobial and antiproliferative agents were investigated. The marine sponge and sediments were collected at different depths (0.9-6 meters) and locations in Florida, including Florida Keys, Port St. Joe in Pensacola, Pensacola Bay, Pensacola Beach, and Fort Pickens...
January 26, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28110506/antibiotic-discovery-throughout-the-small-world-initiative-a-molecular-strategy-to-identify-biosynthetic-gene-clusters-involved-in-antagonistic-activity
#13
Elizabeth Davis, Tyler Sloan, Krista Aurelius, Angela Barbour, Elijah Bodey, Brigette Clark, Celeste Dennis, Rachel Drown, Megan Fleming, Allison Humbert, Elizabeth Glasgo, Trent Kerns, Kelly Lingro, MacKenzie McMillin, Aaron Meyer, Breanna Pope, April Stalevicz, Brittney Steffen, Austin Steindl, Carolyn Williams, Carmen Wimberley, Robert Zenas, Kristen Butela, Hans Wildschutte
The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production...
January 22, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28109059/maintaining-stability-of-the-rumen-ecosystem-is-associated-with-changes-of-microbial-composition-and-epithelial-tlr-signaling
#14
Hong Shen, Zhan Chen, Zanming Shen, Zhongyan Lu
We used the goat as a model to study the effects of rumen microbial composition and epithelial TLR signaling on maintaining rumen stability during exogenous butyrate interference. Six cannulated goats received a rapid intraruminal infusion of 0.1 mol/L potassium phosphate buffer with (BT, n = 3) or without (CO, n = 3) 0.3 g/kg·BW·day sodium butyrate for 28 days. The ruminal pH and the concentration of total SCFA were not affected by the interference. 16S rRNA gene amplicon sequencing revealed a change in microbial composition after the butyrate infusion...
January 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28105780/effect-of-copper-ion-and-soil-humic-acid-on-biodegradation-of-decabromodiphenyl-ether-bde-209-by-pseudomonas-aeruginosa
#15
Yu Liu, Aijun Gong, Lina Qiu, Jingrui Li, Fukai Li
Pseudomonas aeruginosa is a good environmental microorganism capable of degrading decabromodiphenyl ether (BDE-209). This paper studied the effect of Cu(2+) and humic acid (HA) extracted from e-waste contaminated soils on biodegradation of BDE-209 by P. aeruginosa. The adsorption isotherms of Cu(2+) on HA, the crude enzyme activity, cell surface morphology, and biodegradation pathway were also investigated. The results showed that BDE-209 biodegradation by P. aeruginosa was inhibited at Cu(2+) concentrations above 5 mg L(-1) , but exhibited the best effect at the condition of 40 mg L(-1) Cu(2+)  + 3 g L(-1) HA...
January 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28102028/the-involvement-of-msmk-in-pathogenesis-of-the-streptococcus-suis-serotype-2
#16
Mei-Fang Tan, Wan-Quan Liu, Chun-Yan Zhang, Ting Gao, Lin-Lin Zheng, De-Xin Qiu, Lu Li, Rui Zhou
Streptococcus suis serotype 2 (SS2) is an important swine and human pathogen that causes global economic and public health problems. Virulent S. suis strains successfully maintain high bacterial concentrations in host blood and rapidly adapt to challenging environments within hosts. Successful survival in hosts is a major factor influencing the pathogenesis of SS2. We have previously identified that SS2 colonization in mouse brain is possibly affected by the ATPase, MsmK of carbohydrate ATP-binding cassette (ABC) transporters because of carbohydrate utilization...
January 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28097817/revisiting-regulation-of-potassium-homeostasis-in-escherichia-coli-the-connection-to-phosphate-limitation
#17
Hannah Schramke, Vera Laermann, Halina E Tegetmeyer, Andreas Brachmann, Kirsten Jung, Karlheinz Altendorf
Two-component signal transduction constitutes the predominant strategy used by bacteria to adapt to fluctuating environments. The KdpD/KdpE system is one of the most widespread, and is crucial for K(+) homeostasis. In Escherichia coli, the histidine kinase KdpD senses K(+) availability, whereas the response regulator KdpE activates synthesis of the high-affinity K(+) uptake system KdpFABC. Here we show that, in the absence of KdpD, kdpFABC expression can be activated via phosphorylation of KdpE by the histidine kinase PhoR...
January 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28093882/the-gastrointestinal-tract-of-farmed-mink-neovison-vison-maintains-a-diverse-mucosa-associated-microbiota-following-a-3-day-fasting-period
#18
Martin I Bahl, Anne S Hammer, Tove Clausen, Anabelle Jakobsen, Søren Skov, Lars Andresen
Although it is well documented that the gut microbiota plays an important role in health and disease in mammalian species, this area has been poorly studied among carnivorous animals, especially within the mustelidae family. The gastrointestinal tract of carnivores is characterized by its short length and fast transit time, as compared to omnivores and herbivores, which is due to the low level of inherent fermentation. Mink represents an example of this, which have a GI tract only four times the length of the body and a transit time of approximately 4-5 hr...
January 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28088841/intracellular-fate-of-ureaplasma-parvum-entrapped-by-host-cellular-autophagy
#19
Fumiko Nishiumi, Michinaga Ogawa, Yukiko Nakura, Yusuke Hamada, Masahiro Nakayama, Jiro Mitobe, Atsushi Hiraide, Norio Sakai, Makoto Takeuchi, Tamotsu Yoshimori, Itaru Yanagihara
Genital mycoplasmas, including Ureaplasma spp., are among the smallest human pathogenic bacteria and are associated with preterm birth. Electron microscopic observation of U. parvum showed that these prokaryotes have a regular, spherical shape with a mean diameter of 146 nm. U. parvum was internalized into HeLa cells by clathrin-mediated endocytosis and survived for at least 14 days around the perinuclear region. Intracellular U. parvum reached endosomes in HeLa cells labeled with EEA1, Rab7, and LAMP-1 within 1 to 3 hr...
January 15, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28074554/population-genetic-analysis-of-giardia-duodenalis-genetic-diversity-and-haplotype-sharing-between-clinical-and-environmental-sources
#20
Mauricio Durigan, Maisa Ciampi-Guillardi, Ricardo C A Rodrigues, Juliane A Greinert-Goulart, Isabel C V Siqueira-Castro, Diego A G Leal, Sandra Yamashiro, Taís R Bonatti, Maria I Zucchi, Regina M B Franco, Anete P de Souza
Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in various hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas...
January 11, 2017: MicrobiologyOpen
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