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Microbial genomics

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https://www.readbyqxmd.com/read/28720731/an-in-vitro-chicken-gut-model-demonstrates-transfer-of-a-multidrug-resistance-plasmid-from-salmonella-to-commensal-escherichia-coli
#1
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#2
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#3
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#4
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28716113/whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#5
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized...
July 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28716079/the-human-jejunum-has-an-endogenous-microbiota-that-differs-from-those-in-the-oral-cavity-and-colon
#6
Olof H Sundin, Antonio Mendoza-Ladd, Mingtao Zeng, Diana Diaz-Arévalo, Elisa Morales, B Matthew Fagan, Javier Ordoñez, Philip Velez, Nishaal Antony, Richard W McCallum
BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 10(11)-10(12) colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 10(3) to 10(5) CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics...
July 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28715793/monitoring-in-vivo-metabolic-flux-with-a-designed-whole-cell-metabolite-biosensor-of-shikimic-acid
#7
Heng Li, Chaoning Liang, Wei Chen, Jian-Ming Jin, Shuang-Yan Tang, Yong Tao
Knowledge of intracellular metabolite levels is important for the understanding of metabolic flux distributions. Whole-cell biosensors of key metabolites are ideal for the monitoring of carbon flow in important metabolic pathways, thus guiding metabolic engineering for microbial improvement. However, lack of biosensors for metabolites of interests has limited their applications. In this study, a genetically encoded whole-cell biosensor specifically responding to shikimic acid has been developed by screening a site-saturation mutagenesis library of the binding pocket of a uric acid-responsive regulatory protein...
July 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28714894/carbonic-anhydrase-from-porphyromonas-gingivalis-as-a-drug-target
#8
REVIEW
Claudiu T Supuran, Clemente Capasso
Periodontitis originates from a microbial synergy causing the development of a mouth microbial imbalance (dysbiosis), consisting of a microbial community composed of anaerobic bacteria. Most studies concerning the treatment of periodontitis have primarily take into account the Gram-negative bacterium Porphyromonas gingivalis, because it is a prominent component of the oral microbiome and a successful colonizer of the oral epithelium. Here, we focus our attention on the study of the carbonic anhydrases (CAs, EC 4...
July 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28713657/290-metagenome-assembled-genomes-from-the-mediterranean-sea-a-resource-for-marine-microbiology
#9
Benjamin J Tully, Rohan Sachdeva, Elaina D Graham, John F Heidelberg
The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0-50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research...
2017: PeerJ
https://www.readbyqxmd.com/read/28713353/functional-characterization-of-novel-faecalibacterium-prausnitzii-strains-isolated-from-healthy-volunteers-a-step-forward-in-the-use-of-f-prausnitzii-as-a-next-generation-probiotic
#10
Rebeca Martín, Sylvie Miquel, Leandro Benevides, Chantal Bridonneau, Véronique Robert, Sylvie Hudault, Florian Chain, Olivier Berteau, Vasco Azevedo, Jean M Chatel, Harry Sokol, Luis G Bermúdez-Humarán, Muriel Thomas, Philippe Langella
Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713011/the-genomic-and-transcriptomic-analyses-of-serine-proteases-and-their-homologs-in-an-endoparasitoid-pteromalus-puparum
#11
Lei Yang, Zhe Lin, Qi Fang, Jiale Wang, Zhichao Yan, Zhen Zou, Qisheng Song, Gongyin Ye
In insects, serine proteases (SPs) and serine protease homologs (SPHs) constitute a large family of proteins involved in multiple physiological processes such as digestion, development, and immunity. Here we identified 145 SPs and 38 SPHs in the genome of an endoparasitoid, Pteromalus puparum. Gene duplication and tandem repeats were observed in this large SPs/SPHs family. We then analyzed the expression profiles of SP/SPH genes in response to different microbial infections (Gram-positive bacterium Micrococcus luteus, Gram-negative bacterium Escherichia coli, and entomopathogenic fungus Beauveria bassiana), as well as in different developmental stages and tissues...
July 13, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28712783/discovery-and-engineering-of-a-1-butanol-biosensor-in-saccharomyces-cerevisiae
#12
Shuobo Shi, Yook Wah Choi, Huimin Zhao, Meng How Tan, Ee Lui Ang
The present study aimed to develop a universal methodology for the discovery of biosensors sensitive to particular stresses or metabolites by using a transcriptome analysis, in order to address the need for in vivo biosensors to drive the engineering of microbial cell factories. The method was successfully applied to the discovery of 1-butanol sensors. In particular, the genome-wide transcriptome profiling of S. cerevisiae exposed to three similar short-chain alcohols, 1-butanol, 1-propanol, and ethanol, identified genes that were differentially expressed only under the treatment of 1-butanol...
June 23, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28711667/identification-of-three-homologous-latex-clearing-protein-lcp-genes-from-the-genome-of-streptomyces-sp-strain-cfmr-7
#13
Jayaram Nanthini, Su Yean Ong, Kumar Sudesh
Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28710269/molecular-mechanism-and-genetic-determinants-of-buprofezin-degradation
#14
Xueting Chen, Junbin Ji, Leizhen Zhao, Jiguo Qiu, Chen Dai, Weiwu Wang, Jian He, Jiandong Jiang, Qing Hong, Xin Yan
Buprofezin is a widely used insect growth regulator whose residue has been frequently detected in the environment, posing a threat to aquatic organisms and non-target insects. Microorganisms play an important role in the degradation of buprofezin in the natural environment. However, the relevant catabolic pathway has not been fully characterized, and the molecular mechanism of catabolism is still completely unknown. Rhodococcus qingshengii YL-1 can utilize buprofezin as a sole source of carbon and energy for growth...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28709076/coupling-autotrophic-denitrification-with-partial-nitritation-anammox-pna-for-efficient-total-inorganic-nitrogen-removal
#15
Sunayna Dasgupta, Sha Wu, Ramesh Goel
The performance of and the microbial ecology in an integrated lab scale set up comprising of a PN/A bioreactor and an elemental sulfur-supported packed bed autotrophic denitrification (ESSAD) are reported. The PN/A reactor exhibited an average removal rate of 0.56±0.103kgNm(-3)d(-1), whereas the ESSAD reactor removed an average of 0.0018kg NO3(-)-Nm(-3)d(-1). The combined average removal rate was 0.6kgNm(-3)d(-1), yielding an overall total inorganic nitrogen efficiency of 97%. Based on 16S rRNA gene clone libraries from the ESSAD reactor, the extracted Operational Taxonomic Units (OTUs) formed a clade with Thiobacillus denitrificans sp...
June 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28706723/noncontiguous-finished-genome-sequences-and-description-of-bacillus-massiliglaciei-bacillus-mediterraneensis-bacillus-massilinigeriensis-bacillus-phocaeensis-and-bacillus-tuaregi-five-new-species-identified-by-culturomics
#16
F Cadoret, M T Alou, P Afouda, I S Traore, L Bréchard, C Michelle, F Di Pinto, C Andrieu, J Delerce, A Levasseur, P-E Fournier, D Raoult
Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600(T), Bacillus mediterraneensis strain Marseille-P2384(T), Bacillus massilinigeriensis strain Marseille-P2366(T), Bacillus tuaregi strain Marseille-P2489(T) and Bacillus phocaeensis strain SIT16(T) are each the type strain of the corresponding bacterial species...
September 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28705636/a-review-of-bioinformatics-platforms-for-comparative-genomics-recent-developments-of-the-edgar-2-0-platform-and-its-utility-for-taxonomic-and-phylogenetic-studies
#17
J Yu, J Blom, S P Glaeser, S Jaenicke, T Juhre, O Rupp, O Schwengers, S Spänig, A Goesmann
The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics...
July 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28705224/more-than-just-a-gut-feeling-constraint-based-genome-scale-metabolic-models-for-predicting-functions-of-human-intestinal-microbes
#18
REVIEW
Kees C H van der Ark, Ruben G A van Heck, Vitor A P Martins Dos Santos, Clara Belzer, Willem M de Vos
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28700573/crispr-cas-encoding-of-a-digital-movie-into-the-genomes-of-a-population-of-living-bacteria
#19
Seth L Shipman, Jeff Nivala, Jeffrey D Macklis, George M Church
DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome...
July 12, 2017: Nature
https://www.readbyqxmd.com/read/28699403/rna-seq-investigations-of-human-post-mortem-trigeminal-ganglia
#20
Danielle M LaPaglia, Matthew R Sapio, Peter D Burbelo, Jean Thierry-Mieg, Danielle Thierry-Mieg, Stephen J Raithel, Christopher E Ramsden, Michael J Iadarola, Andrew J Mannes
Background The trigeminal ganglion contains neurons that relay sensations of pain, touch, pressure, and many other somatosensory modalities to the central nervous system. The ganglion is also a reservoir for latent herpes virus 1 infection. To gain a better understanding of molecular factors contributing to migraine and headache, transcriptome analyses were performed on postmortem human trigeminal ganglia. Methods RNA-Seq measurements of gene expression were conducted on small sub-regions of 16 human trigeminal ganglia...
January 1, 2017: Cephalalgia: An International Journal of Headache
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