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Microbial bioinformatics

Alberto Ramírez Mata, César Millán Pacheco, José F Cruz Pérez, Martha Minjárez Sáenz, Beatriz E Baca
BACKGROUND: The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Cellular c-di-GMP levels in bacteria are regulated by the opposite enzymatic activities of diguanylate cyclases and phosphodiesterases, which are proteins that have GGDEF and EAL domains, respectively. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants...
March 9, 2018: BMC Microbiology
Rafael R C Cuadrat, Danny Ionescu, Alberto M R Dávila, Hans-Peter Grossart
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations...
2018: Frontiers in Microbiology
Robert C Edgar
Motivation: The 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data. Results: Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms using four accuracy metrics...
February 28, 2018: Bioinformatics
Jun Liu, Qinlu Lin, Xueying Chai, Yunchuan Luo, Ting Guo
BACKGROUND: Phenolic compounds generated in hydrolysis of lignocellulosic materials are major limiting factors for biological production of solvents by Clostridia, but it lacks the attention on the study of adaptation or resistance mechanisms in response to phenolic compounds. RESULTS: Gene Cbei_3304, encoding a hypothetical membrane transport protein, was analyzed by bioinformatic method. After insertional inactivation of the functionally uncertain gene Cbei_3304 in Clostridium beijerinckii NCIMB 8052, resulted in enhanced phenolic compounds tolerance...
March 3, 2018: Microbial Cell Factories
Daniel Garrido-Sanz, Javier Manzano, Marta Martín, Miguel Redondo-Nieto, Rafael Rivilla
Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source...
2018: Frontiers in Microbiology
Haimin Chen, Hongxia Wu, Bin Yan, Hongguang Zhao, Fenghua Liu, Haihua Zhang, Qing Sheng, Fang Miao, Zongsuo Liang
Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5...
February 27, 2018: International Journal of Molecular Sciences
Abu Hena M Kamal, Michael B Fessler, Saiful M Chowdhury
Macrophages are specialized phagocytes that play an essential role in inflammation, immunity, and tissue repair. Profiling the global proteomic response of macrophages to microbial molecules such as bacterial lipopolysaccharide is key to understanding fundamental mechanisms of inflammatory disease. Ethanol is a widely abused substance that has complex effects on inflammation. Reports have indicated that ethanol can activate or inhibit the lipopolysaccharide receptor, Toll-like Receptor 4, in different settings, with important consequences for liver and neurologic inflammation, but the underlying mechanisms are poorly understood...
2018: PloS One
Byunghan Lee, Hyeyoung Min, Sungroh Yoon
Motivation: Metagenomic sequencing has become a crucial tool for obtaining a gene catalogue of operational taxonomic units (OTUs) in a microbial community. A typical metagenomic sequencing produces a large amount of data (often in the order of terabytes or more), and computational tools are indispensable for efficient processing. In particular, error correction in metagenomics is crucial for accurate and robust genetic cataloging of microbial communities. However, many existing error-correction tools take a prohibitively long time and often bottleneck the whole analysis pipeline...
February 20, 2018: Bioinformatics
Peter Rugbjerg, Nils Myling-Petersen, Andreas Porse, Kira Sarup-Lytzen, Morten O A Sommer
A transition toward sustainable bio-based chemical production is important for green growth. However, productivity and yield frequently decrease as large-scale microbial fermentation progresses, commonly ascribed to phenotypic variation. Yet, given the high metabolic burden and toxicities, evolutionary processes may also constrain bio-based production. We experimentally simulate large-scale fermentation with mevalonic acid-producing Escherichia coli. By tracking growth rate and production, we uncover how populations fully sacrifice production to gain fitness within 70 generations...
February 20, 2018: Nature Communications
Catarina Loureiro, Marnix H Medema, John van der Oost, Detmer Sipkema
Microorganisms are Nature's little engineers of a remarkable array of bioactive small molecules that represent most of our new drugs. The wealth of genomic and metagenomic sequence data generated in the last decade has shown that the majority of novel biosynthetic gene clusters (BGCs) is identified from cultivation-independent studies, which has led to a strong expansion of the number of microbial taxa known to harbour BGCs. The large size and repeat sequences of BGCs remain a bioinformatic challenge, but newly developed software tools have been created to overcome these issues and are paramount to identify and select the most promising BGCs for further research and exploitation...
February 14, 2018: Current Opinion in Biotechnology
Tomáš Vetrovský, Petr Baldrian, Daniel Morais, Bonnie Berger
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use...
February 14, 2018: Bioinformatics
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
Daleniece Higgins, Chandan Pal, Irshad M Sulaiman, Chunrong Jia, Tyler Zerwekh, Scot E Dowd, Pratik Banerjee
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA...
March 2018: Food Research International
L E Peachey, R A Molena, T P Jenkins, A Di Cesare, D Traversa, J E Hodgkinson, C Cantacessi
A growing body of evidence, particularly in humans and rodents, supports the existence of a complex network of interactions occurring between gastrointestinal (GI) helminth parasites and the gut commensal bacteria, with substantial effects on both host immunity and metabolic potential. However, little is known of the fundamental biology of such interactions in other animal species. Nonetheless, given the considerable economic losses associated with GI parasites, particularly in livestock and equines, as well as the global threat of emerging anthelmintic resistance, further explorations of the complexities of host-helminth-microbiota interactions in these species are needed...
February 9, 2018: International Journal for Parasitology
Eun-Sook Lee, Eun-Ji Song, So-Young Lee, So-Lim Park, Daeyoung Kim, Daniel Kim, Jae-Hwan Kim, Seong-Il Lim, Young-Do Nam
BACKGROUND: Bentonite is a natural clay mineral with health-promoting effects due to high adsorption abilities with high cation exchange capacity. Previously, we found an anti-obesity effect for the Bgp35b-p bentonite produced in South Korea where its high adsorbent ability of dietary lipids possibly partially removed lipidic environment in the gut (under revision). It hypothesized that Bgp35b-p affects the intestinal microbial community, thus the microbial changes were investigated via the next generation sequencing targeting bacterial 16s rRNA gene and the bioinformatics using QIIME were performed in feces of C57BL/6 male mice fed a HFD with the Bgp35b-p...
February 7, 2018: Journal of the Science of Food and Agriculture
Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E Elias, W Judson Hervey, Thomas McGowan, Thilo Muth, Brook Nunn, Joel Rudney, Alessandro Tanca, Timothy J Griffin, Pratik D Jagtap
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research...
January 31, 2018: Proteomes
Johannes Holert, Erick Cardenas, Lee H Bergstrand, Elena Zaikova, Aria S Hahn, Steven J Hallam, William W Mohn
Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes...
January 30, 2018: MBio
Valeria D'Argenio
The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i...
January 27, 2018: International Journal of Molecular Sciences
Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J Wolfe, Catherine Putonti
Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations amongst bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences, at an abundance far outnumbering eukaryotic viruses...
January 29, 2018: Journal of Bacteriology
Elisabeth Santigli, Martin Koller, Barbara Klug
Oral biofilm and its molecular analysis provide a basis for investigating various dental research and clinical questions. Knowledge of biofilm composition leads to a better understanding of cariogenic and periopathogenic mechanisms. Microbial changes taking place in the oral cavity during childhood are of interest for several reasons. The evolution of the child oral microbiota and shifts in its composition need to be analyzed further to understand and possibly prevent the onset of disease. At the same time, advanced knowledge of the natural composition of oral biofilm is needed...
December 31, 2017: Journal of Visualized Experiments: JoVE
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