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Results for “Microbiology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 325 records · Page 18Linked to original sources

bioRxiv2016

Capture of Vibrio cholerae by charged polymers inhibits pathogeniciy by inducing a sessile lifestyle

Vibrio cholerae, the causative agent of cholera, is an abundant environmental bacterium that can efficiently colonize the intestinal tract and trigger severe diarrheal illness. Motility, and the production of colonization factors and cholera toxin, are fundamental for the establishment of disease. In the aquatic environment, V. cholerae persists by forming avirulent biofilms on zooplankton, phytoplankton and chitin debris. Here, we describe the formation of artificial, biofilm-like communities, driven by exposure of planktonic bacteria to synthetic polymers. This recruitment is extremely rapid and charge-driven, and leads to the formation of initial \"seed clusters\" which then recruit additional bacteria to extend in size. Bacteria that become entrapped in these \"forced communities\" undergo transcriptional changes in motility and virulence genes, and phenotypically mimic features of environmental biofilm communities by forming a matrix that contains polysaccharide and extracellular DNA. As a result of this lifestyle transition, pathogenicity and in vivo host colonization decrease. These findings highlight the potential of synthetic polymers to disarm pathogens by modulating their lifestyle, without creating selective pressure favoring the emergence of antimicrobial resistant strains.

Microbiology↗

bioRxiv2016

Cohort Specific Effects of Cereal-bar Supplementation in Overweight Patients With or Without Type 2 Diabetes Mellitus

The importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand diet-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-iabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g {beta}-lucan on their habitual diet for 30 days. Fecal bacterial communities in an age-atched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to cereal-bar supplementation are cohort specific and this should be considered when manipulating the microbiome via diet supplementation.

Microbiology↗

bioRxiv2016

Small molecules with antibiofilm, antivirulence and antibiotic synergy activities against Pseudomonas aeruginosa.

Biofilm formation is a universal bacterial strategy for long-term survival in nature and during infections. Biofilms are dense microbial communities enmeshed within a polymeric extracellular matrix that protects bacteria from antibiotic exposure and the immune system and thus contribute to chronic infections. Pseudomonas aeruginosa is an archetypal biofilm-forming organism that utilizes a biofilm growth strategy to cause chronic lung infections in Cystic Fibrosis (CF) patients. The extracellular matrix of P. aeruginosa biofilms is comprised mainly of exopolysaccharides (EPS) and DNA. Both mucoid and non-mucoid isolates of P. aeruginosa produces the Pel and Psl EPS, each of which have important roles in antibiotic resistance, biofilm formation and immune evasion. Given the central importance of the Pel and Psl EPS in biofilm structure, they are attractive targets for novel anti-infective compounds. In this study we used a high throughput gene expression screen to identify compounds that repress expression of pel and psl genes as measured by transcriptional lux fusions. Testing of the pel/psl repressors demonstrated an antibiofilm activity against microplate and flow chamber biofilms formed by wild type and hyperbiofilm forming strains. To determine the potential role of EPS in virulence, mutants in pel/psl were shown to have reduced virulence in the feeding behavior and slow killing virulence assays in Caenorhabditis elegans. The antibiofilm molecules also reduced P. aeruginosa PAO1 virulence in the nematode slow killing model. Importantly, the combination of antibiotics and antibiofilm compounds were synergistic in killing P. aeruginosa biofilms. These small molecules represent a novel anti-infective strategy for the possible treatment of chronic P. aeruginosa infections.\n\nAuthor summaryBacteria use the strategy of growing as a biofilm to promote long-term survival and therefore to cause chronic infections. One of the best examples is Pseudomonas aeruginosa and the chronic lung infections in individuals with Cystic Fibrosis (CF). Biofilms are generally a dense community of bacteria enmeshed in an extracellular matrix that protects bacteria from numerous environmental stresses, including antibiotics and the immune system. In this study we developed an approach to identify P. aeruginosa biofilm inhibitors by repressing the production of the matrix exopolysaccharide (EPS) polymers. Bacteria treated with compounds and then fed to the nematode also had showed reduced virulence by promoting nematode survival. To tackle the problem of biofilm tolerance of antibiotics, the compounds identified here also had the beneficial property of increasing the biofilm sensitivity to different classes of antibiotics. The compounds disarm bacteria but they do not kill or limit growth like antibiotics. We provide further support that disarming P. aeruginosa may be a critical anti-infective strategy that limits the development of antibiotic resistance, and provides a new way for treating chronic infections.

Microbiology↗

bioRxiv2016

Stochastic Assembly Produces Heterogeneous Communities in the C. elegans Intestine

Author SummaryHost-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this variation. In this manuscript, we demonstrate experimentally how randomness in colonization can result in large differences in the composition of host-associated bacterial communities, using the nematode worm C. elegans as a tractable host model. Here, the amount of variation between individual communities is a function of two rates relevant to how bacteria colonize the host intestine, the colonization rate and the birth rate. We can therefore control the degree of variation between communities by controlling the colonization rate, using the amount of bacteria presented to the worms to control the rate at which migrants enter the intestine. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains at low colonization rates, we are able to produce noise-induced bistability in this system, where each community is dominated by bacteria of only one color. These results demonstrate the potential importance of noise as a driver of variation between communities and highlight the utility of the simple model organism C. elegans for studying questions relevant to host-associated microbial communities.\n\nAbstractHost-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here we demonstrate that stochastic bacterial community assembly in the C. elegans intestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. These results demonstrate that demographic noise is a potentially important driver of diversity in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

Microbiology↗

bioRxiv2016

Experimental estimation of the effects of all amino-acid mutations to HIV Env

HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIVs most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIVs growth in cell culture. We compare our experimental measurements of each sites preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. We show that some regions of Env have a high inherent tolerance to mutation, whereas other regions (such as epitopes of broadly neutralizing antibodies) have a significantly reduced capacity to tolerate mutations. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Envs evolution.

Microbiology↗

bioRxiv2016

Rapid resistome mapping using nanopore sequencing

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.

Microbiology↗

bioRxiv2016

Direct correlation between motile behavior and protein abundance in single cells

Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

Microbiology↗

bioRxiv2016

Genome Integration and Reactivation of the Virophage Mavirus In the Marine Protozoan Cafeteria roenbergensis

Endogenous viral elements (EVEs) are increasingly found in eukaryotic genomes1, yet little is known about their origins, dynamics, or function. Here, we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defense system. We found that the virophage mavirus2, a parasite of the giant Cafeteria roenbergensis virus (CroV)3, integrates at multiple sites within the nuclear genome of the marine protozoan Cafeteria roenbergensis. The endogenous mavirus is structurally and genetically similar to the eukaryotic Maverick/Polinton DNA transposons4,5 and endogenous polintoviruses6. Provirophage genes are not constitutively expressed, but are specifically activated by superinfection with CroV, which induces the production of infectious mavirus particles. Virophages inhibit the replication of giant viruses and a beneficial effect of provirophages on their host cells has been hypothesized2,7. We found that provirophage-carrying cells are not directly protected from CroV; however, lysis of these cells releases reactivated mavirus particles that are then able to suppress CroV replication and enhance host survival of other CroV-infected flagellate populations in a dose-dependent manner. The host-parasite interaction described here involves an altruistic aspect that is unique among microbes. Our results demonstrate a direct link between mavirus and Maverick/Polinton elements and suggest that provirophages can defend natural protist populations against infection by giant viruses.

Microbiology↗

bioRxiv2016

290 Metagenome-assembled Genomes from the Mediterranean Sea: Ongoing Effort to Generate Genomes from the Tara Oceans Dataset

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 high-quality 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 high-quality genomes to open-access repositories for the scientific community to use in ongoing research.

Microbiology↗

bioRxiv2016

One-cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAY extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.

Microbiology↗

bioRxiv2016

What is the link between stringent response, endoribonuclease encoding Type II Toxin-Antitoxin systems and persistence?

Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is Toxin-Antitoxin systems (TAS) which are also implicated in a wide range of stress-related phenomena. In a report (Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150) an interesting link between ppGpp mediated stringent response, TAS and persistence was proposed. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for Lon-dependent degradation of YefM, the antitoxin of YefM/YoeB TAS. The {Delta}10 strain, an Escherichia coli MG1655 derivative in which the ten TAS are deleted, is more sensitive to Ciprofloxacin and Ampicillin compared to wild-type MG1655. Furthermore, we show that the {Delta}10 strain has relatively lower fitness compared to the wild type and hence, we argue that the implications based on this strain are void. We conclude that there is no direct and specific link between stringent response and the regulation of TAS. The link between TAS and persistence is inconclusive due to altered fitness of {Delta}10 strain and hence requires thorough inspection and debate.\n\nImportanceA model connecting stringent response, endoribonuclease encoding Type II Toxin-Antitoxin systems (TAS) and persistence is widely propagated. It states that \"accumulation of ppGpp results in accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxin rendering toxins free to induce persistence\". This work presents a contradiction to and challenges the model. Experimental evidence, literature survey as well as rationale are provided to show that inorganic polyphosphate is not required for the degradation of YefM, the antitoxin in YefM/YoeB TAS. The {Delta}10 strain is relatively more sensitive to Ciprofloxacin and Ampicillin as well as has lowered fitness. This is likely because of the polar effects on the adjacent genes caused by the genetic manipulation of multiple TAS loci.

Microbiology↗

bioRxiv2016

Novel blaKPC-carrying species identified in the hospital environment

blaKPC, encoding one of five dominant global carbapenemase families, is increasingly identified in environmental species difficult to characterize using routine diagnostic methods, with epidemiological and clinical implications. During environmental hospital infection prevention and control investigations (Manchester, UK) we used whole genome sequencing to confirm species identification for isolates infrequently associated with blaKPC and/or difficult to classify by MALDI-ToF. Four previously undescribed blaKPC-carrying species were identified from the hospital environment, including a putative, novel Enterobacter species.

Microbiology↗

bioRxiv2016

Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology

Conceptual models suggest certain microorganisms (e.g., the red complex) are indicative of a specific disease state (e.g., periodontitis); however, recent studies have questioned the validity of these models. Here, the abundances of 500+ microbial species were determined in 16 patients with clinical signs of one of the following oral conditions: periodontitis, established caries, edentulism, and oral health. Our goal was to determine if the abundances of certain microorganisms reflect dysbiosis or a specific clinical condition that could be used as a signature for dental research. Microbial abundances were determined by the analysis of 138,718 calibrated probes using Gene Meter methodology. Each 16S rRNA gene was targeted by an average of 194 unique probes (n=25 nt). The calibration involved diluting pooled gene target samples, hybridizing each dilution to a DNA microarray, and fitting the probe intensities to adsorption models. The fit of the model to the experimental data was used to assess individual and aggregate probe behavior; good fits (R2>0.90) were retained for back-calculating microbial abundances from patient samples. The abundance of a gene was determined from the median of all calibrated individual probes or from the calibrated abundance of all aggregated probes. With the exception of genes with low abundances (< 2 arbitrary units), the abundances determined by the different calibrations were highly correlated (r [~]1.0). Seventeen genera were classified as signatures of dysbiosis because they had significantly higher abundances in patients with periodontitis and edentulism when contrasted with health. Similarly, 13 genera were classified as signatures of periodontitis, and 14 genera were classified as signatures of edentulism. The signatures could be used, individually or in combination, to assess the clinical status of a patient (e.g., evaluating treatments such as antibiotic therapies). Comparisons of the same patient samples revealed high false negatives (45%) for next-generation-sequencing results and low false positives (7%) for Gene Meter results.

Microbiology↗

bioRxiv2016

Genome-wide prediction of microRNAs in Zika virus genomes reveals possible interactions with human genes involved in the nervous system development

Zika virus (ZIKV) is a member of the family Flaviviridae. In 2015, ZIKV triggered a large epidemic in Brazil and spread across Latin America. In November of that year, the Brazilian Ministry of Health reported a 20-fold increase in cases of neonatal microcephaly, which corresponds geographically and temporally to the ZIKV outbreak. ZIKV was isolated from the brain tissue of a fetus diagnosed with microcephaly, and recent studies in mice models revealed that ZIKV infection may cause brain defects by influencing brain cell developments. Unfortunately, the mechanisms by which ZIKV alters neurophysiological development remain unknown. MicroRNAs (miRNAs) are small noncoding RNAs that regulate post-transcriptional gene expression by translational repression. In order to gain insight into the possible role of ZIKV-mediated miRNA signaling dysfunction in brain-tissue development, we computationally predicted new miRNAs encoded by the ZIKV genome and their effective hybridization with transcripts from human genes previously shown to be involved in microcephalia. The results of these studies suggest a possible role of these miRNAs on the expression of human genes associated with this disease. Besides, a new ZIKV miRNA was predicted in the 3stem loop (3 SL) of the 3untranslated region (3UTR) of the ZIKV genome, suggesting the role of the 3UTR of flaviviruses as a source of miRNAs.

Microbiology↗

bioRxiv2016

Mating promotes lactic-acid gut bacteria in a gift-giving insect

Mating is a ubiquitous social interaction with the potential to influence the microbiome by facilitating transmission, modifying host physiology, and in species where males donate nuptial gifts to females, altering diet. We manipulated mating and nuptial gift consumption in two insects that differ in nuptial gift size, the Mormon cricket Anabrus simplex and the decorated cricket Gryllodes sigillatus, with the expectation that larger gifts are more likely to affect the gut microbiome. Surprisingly, mating, but not nuptial gift consumption, affected bacterial community structure, and only in Mormon crickets. The change in structure was due to a precipitous drop in the abundance of lactic-acid bacteria in unmated females, a taxon known for their beneficial effects on nutrition and immunity. Mating did not affect phenoloxidase or lysozyme-like antibacterial activity in either species, suggesting that any physiological response to mating on host-microbe interactions is decoupled from the systemic immunity. Protein supplementation also did not affect the gut microbiome in decorated crickets, suggesting that insensitivity of gut microbes to dietary protein could contribute to the lack of an effect of nuptial gift consumption. Our study provides experimental evidence that sexual interactions can affect the microbiome and suggests mating can promote beneficial gut bacteria.

Microbiology↗

bioRxiv2016

Modeling time-series data from microbial communities

As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (e.g. skin, soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open, thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but given the big data nature of these studies, there are currently no methods capable of utilizing the breadth of the data to infer ecological interactions from these longitudinal data. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that 1) takes advantage of the fact that the data are time series; 2) constrains estimates to allow for the possibility of many more interactions than data; and 3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

Microbiology↗

bioRxiv2016

Root hair-endophyte stacking (RHESt) in an ancient Afro-Indian crop creates an unusual physico-chemical barrier to trap pathogen(s)

The ancient African crop, finger millet, has broad resistance to pathogens including the toxigenic fungus Fusarium graminearum. Here we report the discovery of a novel plant defence mechanism, resulting from an unusual symbiosis between finger millet and a root-inhabiting bacterial endophyte, M6 (Enterobacter sp.). Seed-coated M6 swarms towards Fusarium attempting to penetrate root epidermis, induces growth of root hairs which then bend parallel to the root axis, then forms biofilm-mediated microcolonies, resulting in a remarkable, multi-layer root hair-endophyte stack (RHESt). RHESt results in a physical barrier that prevents entry and/or traps F. graminearum which is then killed. Thus M6 creates its own specialized killing microhabitat. M6 killing requires c-di-GMP-dependent signalling, diverse fungicides and xenobiotic resistance. Further molecular evidence suggests long-term host-endophyte-pathogen co-evolution. The end-result of this remarkable symbiosis is reduced DON mycotoxin, potentially benefiting millions of subsistence farmers and livestock. RHESt demonstrates the value of exploring ancient, orphan crop microbiomes.

Microbiology↗

bioRxiv2016

Bovine Lactoferrin Activity Against Chikungunya and Zika Viruses

Chikungunya (CHIKV) and Zika (ZIKV) viruses are two arboviruses which have recently broken their sylvatic isolation and gone into a rampant spreading among humans in some urban areas of the world, specially in Latin America. Given the huge burden that Chikungunya and Zika fevers impose to public health in the affected countries and the lack of effective interventions against them, the aim of this work was to evaluate the antiviral potential of bovine lactoferrin (bLf) - an iron-binding glycoprotein with broad-spectrum antimicrobial properties - in both CHIKV and ZIKV infections. The general antiviral activity of bLf was assessed by plaque assays, and the inhibitory effects of the protein on specific stages of virus infecion was evaluated by immunofluorescence and nucleic acid quantification assays. Our data show that bLf exerts a dose-dependent strong inhibitory effect on the infection of Vero cells by the aforementioned arboviruses, reducing their infection efficiency in up to nearly 80%, with no significant cytotoxicity, and such antiviral activity occurs at the levels of binding and replication of the virus particles. Taken together, these findings reveal that bLf antimicrobial properties are extendable to CHIKV and ZIKV, underlining a generic inhibition mechanism that can be explored to develop a potential strategy against their infections.

Microbiology↗