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Bacteria evolution

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https://www.readbyqxmd.com/read/28930173/polyphenols-from-root-tubercles-and-grains-cropped-in-brazil-chemical-and-nutritional-characterization-and-their-effects-on-human-health-and-diseases
#1
REVIEW
Diego Dos Santos Baião, Cyntia Silva de Freitas, Laidson Paes Gomes, Davi da Silva, Anna Carolina N T F Correa, Patricia Ribeiro Pereira, Eduardo Mere Del Aguila, Vania Margaret Flosi Paschoalin
Throughout evolution, plants have developed the ability to produce secondary phenolic metabolites, which are important for their interactions with the environment, reproductive strategies and defense mechanisms. These (poly)phenolic compounds are a heterogeneous group of natural antioxidants found in vegetables, cereals and leguminous that exert beneficial and protective actions on human health, playing roles such as enzymatic reaction inhibitors and cofactors, toxic chemicals scavengers and biochemical reaction substrates, increasing the absorption of essential nutrients and selectively inhibiting deleterious intestinal bacteria...
September 20, 2017: Nutrients
https://www.readbyqxmd.com/read/28928474/using-experimental-evolution-to-identify-druggable-targets-that-could-inhibit-the-evolution-of-antimicrobial-resistance
#2
Heer H Mehta, Amy G Prater, Yousif Shamoo
With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics...
September 20, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28928209/combining-comprehensive-analysis-of-off-site-lambda-phage-integration-with-a-crispr-based-means-of-characterizing-downstream-physiology
#3
Yu Tanouchi, Markus W Covert
During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28925975/new-insights-into-the-genome-organization-of-yeast-killer-viruses-based-on-atypical-killer-strains-characterized-by-high-throughput-sequencing
#4
Manuel Ramírez, Rocío Velázquez, Antonio López-Piñeiro, Belén Naranjo, Francisco Roig, Carlos Llorens
Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed...
September 19, 2017: Toxins
https://www.readbyqxmd.com/read/28923945/antagonism-correlates-with-metabolic-similarity-in-diverse-bacteria
#5
Jakob Russel, Henriette L Røder, Jonas S Madsen, Mette Burmølle, Søren J Sørensen
In the Origin of Species, Charles R. Darwin [Darwin C (1859) On the Origin of Species] proposed that the struggle for existence must be most intense among closely related species by means of their functional similarity. It has been hypothesized that this similarity, which results in resource competition, is the driver of the evolution of antagonism among bacteria. Consequently, antagonism should mostly be prevalent among phylogenetically and metabolically similar species. We tested the hypothesis by screening for antagonism among all possible pairwise interactions between 67 bacterial species from 8 different environments: 2,211 pairs of species and 4,422 interactions...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922872/ancient-occasional-host-switching-of-maternally-transmitted-bacterial-symbionts-of-chemosynthetic-vesicomyid-clams
#6
Genki Ozawa, Shigeru Shimamura, Yoshihiro Takaki, Kiyotaka Takishita, Tetsuro Ikuta, James P Barry, Tadashi Maruyama, Katsunori Fujikura, Takao Yoshida
Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28921884/structural-characterization-and-functional-analysis-of-cystathionine-%C3%AE-synthase-an-enzyme-involved-in-the-reverse-transsulfuration-pathway-of-bacillus-anthracis
#7
Suneeta Devi, Syed Arif Abdul Rehman, Khaja Faisal Tarique, Samudrala Gourinath
The reverse transsulfuration pathway has been reported to produce cysteine from homocysteine in eukaryotes ranging from protozoans to mammals while bacteria and plants produce cysteine via a de-novo pathway. Interestingly, the bacterium Bacillus anthracis includes enzymes of the reverse transsulfuration pathway viz. cystathionine β-synthase (BaCBS, previously annotated to be an O-acetylserine sulfhydrylase (OASS)) and cystathionine γ-lyase. Here, we report the structure of BaCBS at a resolution of 2.2 Å...
September 16, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#8
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28914794/effects-of-probiotics-prebiotics-and-synbiotics-on-human-health
#9
REVIEW
Paulina Markowiak, Katarzyna Śliżewska
The human gastrointestinal tract is colonised by a complex ecosystem of microorganisms. Intestinal bacteria are not only commensal, but they also undergo a synbiotic co-evolution along with their host. Beneficial intestinal bacteria have numerous and important functions, e.g., they produce various nutrients for their host, prevent infections caused by intestinal pathogens, and modulate a normal immunological response. Therefore, modification of the intestinal microbiota in order to achieve, restore, and maintain favourable balance in the ecosystem, and the activity of microorganisms present in the gastrointestinal tract is necessary for the improved health condition of the host...
September 15, 2017: Nutrients
https://www.readbyqxmd.com/read/28912769/adaptation-of-surface-associated-bacteria-to-the-open-ocean-a-genomically-distinct-subpopulation-of-phaeobacter-gallaeciensis-colonizes-pacific-mesozooplankton
#10
Heike M Freese, Anika Methner, Jörg Overmann
The marine Roseobacter group encompasses numerous species which occupy a large variety of ecological niches. However, members of the genus Phaeobacter are specifically adapted to a surface-associated lifestyle and have so far been found nearly exclusively in disjunct, man-made environments including shellfish and fish aquacultures, as well as harbors. Therefore, the possible natural habitats, dispersal and evolution of Phaeobacter spp. have largely remained obscure. Applying a high-throughput cultivation strategy along a longitudinal Pacific transect, the present study revealed for the first time a widespread natural occurrence of Phaeobacter in the marine pelagial...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28910985/yeast-bacteria-competition-induced-new-metabolic-traits-through-large-scale-genomic-rearrangements-in-lachancea-kluyveri
#11
Nerve Zhou, Samuele Bottagisi, Michael Katz, Joseph Schacherer, Anne Friedrich, Zoran Gojkovic, Krishna B S Swamy, Wolfgang Knecht, Concetta Compagno, Jure Piškur
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations...
September 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28904122/evolution-of-polymer-formation-within-the-actin-superfamily
#12
Patrick R Stoddard, Tom A Williams, Ethan Garner, Buzz Baum
While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes...
September 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28893783/evolution-of-antibiotic-resistance-without-antibiotic-exposure
#13
Anna Knöppel, Joakim Näsvall, Dan I Andersson
Antibiotic use is the main driver in the emergence of antibiotic resistance. Another unexplored possibility is that resistance evolves coincidentally in response to other selective pressures. We show that selection in the absence of antibiotics can co-select for decreased susceptibility to several antibiotics. Thus, genetic adaptation of bacteria to natural environments may drive resistance evolution by generating a pool of resistance mutations that selection could act on to enrich resistant mutants when antibiotic exposure occurs...
September 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28893176/the-path-to-re-evolve-cooperation-is-constrained-in-pseudomonas-aeruginosa
#14
Elisa T Granato, Rolf Kümmerli
BACKGROUND: A common form of cooperation in bacteria is based on the secretion of beneficial metabolites, shareable as public good among cells within a group. Because cooperation can be exploited by "cheating" mutants, which contribute less or nothing to the public good, there has been great interest in understanding the conditions required for cooperation to remain evolutionarily stable. In contrast, much less is known about whether cheats, once fixed in the population, are able to revert back to cooperation when conditions change...
September 11, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28892759/bioelectrochemical-sulphate-reduction-on-batch-reactors-effect-of-inoculum-type-and-applied-potential-on-sulphate-consumption-and-ph
#15
Manuel A Gacitúa, Enyelbert Muñoz, Bernardo González
Microbial electrolysis batch reactor systems were studied employing different conditions, paying attention on the effect that biocathode potential has on pH and system performance, with the overall aim to distinguish sulphate reduction from H2 evolution. Inocula from pure strains (Desulfovibrio paquesii and Desulfobacter halotolerans) were compared to a natural source conditioned inoculum. The natural inoculum possess the potential for sulphate reduction on serum bottles experiments due to the activity of mutualistic bacteria (Sedimentibacter sp...
August 25, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28892294/nuclease-activity-gives-an-edge-to-host-defense-peptide-piscidin-3-over-piscidin-1-rendering-it-more-effective-against-persisters-and-biofilms
#16
M Daben J Libardo, Ali Adem Bahar, Buyong Ma, Riqiang Fu, Laura E McCormick, Jun Zhao, Scott A McCallum, Ruth Nussinov, Dacheng Ren, Alfredo M Angeles-Boza, Myriam L Cotten
Host defense peptides (HDPs) feature evolution-tested potency against life-threatening pathogens. While piscidin 1 (p1) and piscidin 3 (p3) are homologous and potent fish HDPs, only p1 is strongly membranolytic. Here, we hypothesize that another mechanism imparts p3 strong potency. We demonstrate that the N-termini of both peptides coordinate Cu(2+) and p3-Cu cleaves isolated DNA at a rate on par with free Cu(2+) but significantly faster than p1-Cu. On planktonic bacteria, p1 is more antimicrobial but only p3 features copper-dependent DNA cleavage...
September 11, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28888066/the-interactions-between-gut-microbiota-and-entomopathogenic-fungi-a-potential-approach-for-biological-control-of-blattella-germanica-l
#17
Fan Zhang, Xiao X Sun, Xian C Zhang, Shuo Zhang, Jie Lu, Yong M Xia, Yan H Huang, Xue J Wang
BACKGROUND: Metarhizium anisopliae and Beauveria bassiana mainly infect insects through the cuticle; gut infection occasionally occurs. Microorganisms existing in the gut may play a crucial role in the evolution and ecology of host defenses to fungal pathogens. To evaluate whether the gut bacteria participate in antifungal activity, and to determine their role in host protection, the interactions between gut bacteria and M. anisopliae and the diversity of gut microbiota in cockroaches were studied...
September 9, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28887484/differential-degeneration-of-the-actagt-sequence-among-salmonella-a-reflection-of-distinct-nucleotide-amelioration-patterns-during-bacterial-divergence
#18
Le Tang, Emilio Mastriani, Yu-Jie Zhou, Songling Zhu, Xin Fang, Yang-Peng Liu, Wei-Qiao Liu, Yong-Guo Li, Randal N Johnston, Zheng Guo, Gui-Rong Liu, Shu-Lin Liu
When bacteria diverge, they need to adapt to the new environments, such as new hosts or different tissues of the same host, by accumulating beneficial genomic variations, but a general scenario is unknown due to the lack of appropriate methods. Here we profiled the ACTAGT sequence and its degenerated forms (i.e., hexa-nucleotide sequences with one of the six nucleotides different from ACTAGT) in Salmonella to estimate the nucleotide amelioration processes of bacterial genomes. ACTAGT was mostly located in coding sequences but was also found in several intergenic regions, with its degenerated forms widely scattered throughout the bacterial genomes...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886124/identification-and-genomic-comparison-of-temperate-bacteriophages-derived-from-emetic-bacillus-cereus
#19
Peiling Geng, Shen Tian, Zhiming Yuan, Xiaomin Hu
Cereulide-producing Bacillus cereus isolates can cause serious emetic (vomiting) syndrome and even acute lethality. As mobile genetic elements, the exploration of prophages derived from emetic B. cereus isolates will help in our understanding of the genetic diversity and evolution of these pathogens. In this study, five temperate phages derived from cereulide-producing B. cereus strains were induced, with four of them undergoing genomic sequencing. Sequencing revealed that they all belong to the Siphoviridae family, but presented in different forms in their hosts...
2017: PloS One
https://www.readbyqxmd.com/read/28886010/mobility-can-promote-the-evolution-of-cooperation-via-emergent-self-assortment-dynamics
#20
Jaideep Joshi, Iain D Couzin, Simon A Levin, Vishwesha Guttal
The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing...
September 2017: PLoS Computational Biology
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