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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 253 records · Page 14Linked to original sources

bioRxiv2016

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening

BackgroundThere is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the gut microbiota can complement the fecal occult blood test and fecal immunochemical test (FIT). However, a barrier to microbiota-based screening is the need to collect and store a patients stool sample.\n\nMethodsUsing stool samples collected from 404 patients we tested whether the residual buffer containing resuspended feces in FIT cartridges could be used in place of intact stool samples.\n\nResultsWe found that the bacterial DNA isolated from FIT cartridges largely recapitulated the community structure and membership of patients stool microbiota and that the abundance of bacteria associated with CRC were conserved. We also found that models for detecting CRC that were generated using bacterial abundances from FIT cartridges were equally predictive as models generated using bacterial abundances from stool.\n\nConclusionsThese findings demonstrate the potential for using residual buffer from FIT cartridges in place of stool for microbiota-based screening for CRC. This may reduce the need to collect and process separate stool samples and may facilitate combining FIT and microbiota-based biomarkers into a single test. Additionally, FIT cartridges could constitute a novel data source for studying the role of the microbiome in cancer and other diseases.

Microbiology↗

bioRxiv2016

Inventory of cultivatable populations of S-cycling, fermentative, Fe-reducing, and aerobic heterotrophic bacteria from salt marsh sediments.

A survey was carried out of the dominant chemotrophic groups of bacteria inhabiting surface salt marsh sediments in the Virginia Coastal Reserve (VCR) on the Atlantic coast of Virginia. Total direct cell counts were carried out on all samples. Aerobic heterotrophs, sulfur oxidizers, sulfate reducing bacteria (SRB), sulfur disproportionaters, Fe-reducing (FeRB) and fermentative bacteria were all quantified by most probable number (MPN) at four different sites that ranged in spatial scale from a few meters to 15 km apart. The sites were sampled every 3 - 4 months over a two year period. Total cell counts were quite consistent temporally at each of the sites, and ranged from a high of 1.4 x 1010 cells. gdw-1 to a low of 8 x 108 cells. gdw-1. Recoveries of all culturable bacteria were also site dependent and ranged from a minimum of 0.4% to a maximum of 40% of the total cell count. Aerobic bacteria were the dominant recovered population at all of the sites, followed by sulfur-oxidizing bacteria. Together these two groups accounted for >75% of the total recovered bacteria at each of the sites. The populations of anaerobic groups fluctuated significantly; S-disproportionating and SRB were most abundant followed by FeRB and fermenters. On average, all the anaerobes were in the same order of magnitude of abundance (107 cells. gdw-1). Overall, these results suggest that aerobic bacteria consistently predominated in the top 10 cm of the marsh sediments, and that autotrophy related to sulfur oxidation and disproportionation may be important, but under studied processes in salt marsh ecosystems.

Microbiology↗

bioRxiv2016

mazEF mediated programmed cell death in Escherichia coli: is it?

Toxin-antitoxins systems (TAS) are prokaryotic operons containing two small overlapping genes which encode two components referred to as Toxin and Antitoxin. Involvement of TAS in bacterial programmed cell death (PCD) is highly controversial. MazEF, a typical type II TAS, is particularly implicated in mediating PCD in Escherichia coli. Hence, we compared the metabolic fitness and stress tolerance of E. coli strains (MC4100 and its mazEF- derivative) which were extensively used by proponents of mazEF- mediated PCD. We found that both the strains are deficient in relA gene and that the{Delta} mazEF strain has lower fitness and stress tolerance compared to wild type MC4100. Furthermore, these strains are likely not isogenic. We could not reproduce mazEF mediated PCD which emphasizes the need for skeptic approach to the PCD hypothesis.

Microbiology↗

bioRxiv2016

Time-resolved dual RNA-Seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection

Streptococcus pneumoniae (pneumococcus) is the main etiological agent of pneumonia. Pneumococcal pneumonia is initiated by bacterial adherence to lung epithelial cells. Infection to the epithelium is a disruptive interspecies interaction involving numerous transcription-mediated processes. Revealing transcriptional changes may provide valuable insights into pneumococcal disease. Dual RNA-Seq allows simultaneous monitoring of the transcriptomes of both host and pathogen. Here, we developed a time-resolved infection model of human lung alveolar epithelial cells by S. pneumoniae and assessed transcriptome changes by dual RNA-Seq. Our data provide new insights into host-microbe interactions and show that the epithelial glutathione-detoxification pathway is activated by bacterial presence. We observed that adherent pneumococci, not free-floating bacteria, access host-associated carbohydrates and repress innate immune responses. In conclusion, we provide a dynamic dual-transcriptomics overview of early pneumococcal infection with easy online access (http://dualrnaseq.molgenrug.nl). Further database exploration may expand our understanding of epithelial-pneumococcal interaction, leading to novel antimicrobial strategies.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC=\"FIGDIR/small/048959_fig7.gif\" ALT=\"Figure 7\">\nView larger version (60K):\norg.highwire.dtl.DTLVardef@351367org.highwire.dtl.DTLVardef@8cd781org.highwire.dtl.DTLVardef@985c96org.highwire.dtl.DTLVardef@e6b6a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Microbiology↗

bioRxiv2016

First detection of Zika virus in neotropical primates in Brazil: a possible new reservoir.

Samples from sera and oral swabs from fifteen marmosets (Callithrix jacchus) and nine capuchin-monkeys (Sapajus libidinosus) captured in Ceara State in Brazil were tested for Zika virus. Samples were positive by Real time PCR and sequencing of the amplified product from a capuchin monkey showed 100% similarity to other ZIKV from South America. This is the first report on ZIKV detection among Neotropical primates.

Microbiology↗

bioRxiv2016

The Pseudomonas aeruginosa PSL polysaccharide is a social but non-cheatable trait in biofilms

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment and which are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either co-operative public goods, or as traits that provide a competitive advantage. Here we empirically test the co-operative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that: (1) PSL is not metabolically costly to produce; (2) PSL provides population level benefits in biofilms, for both growth and antibiotic tolerance; (3) the benefits of PSL production are social and are shared with other cells; (4) the benefits of PSL production appear to be preferentially directed towards cells which produce PSL; (5) cells which do not produce PSL are unable to successfully exploit cells which produce PSL. Taken together, this suggests that PSL is a social but relatively non-exploitable trait, and that growth within biofilms selects for PSL-producing strains, even when multiple strains can interact (low relatedness).

Microbiology↗

bioRxiv2016

Lactobacillus plantarum is a pathobiont for adult Drosophila.

The microbiome of Drosophila promotes intestinal stem cell division through evolutionarily conserved biochemical pathways. As such, axenic flies have lower rates of gut stem cell division than age-matched wild type counterparts. Additionally, flies with a full consortium of symbiotic bacteria are shorter lived than those maintained in the absence of a microbiome. However, we do not know if stem cell division is essential for symbiont-dependent regulation of adult fly lifespan. To determine if individual symbionts cause aging-dependent death in Drosophila, we examined the impacts of common symbionts on host longevity. In this study, we found that mono-association of adult Drosophila with Lactobacillus plantarum, a widely reported fly symbiont, and member of the probiotic Lactobacillus genus, curtails adult longevity relative to germ-free counterparts. However, the effects of plantarum on lifespan were independent of intestinal aging. Instead, we found that association with plantarum causes an extensive intestinal pathology within the host, characterized by loss of intestinal stem cells, impaired epithelial renewal, and a gradual erosion of epithelial integrity. Our study uncovers an unknown aspect of Lactobacillus plantarum-Drosophila interactions, and establishes a simple model to characterize symbiont-dependent disruption of intestinal homeostasis.

Microbiology↗

bioRxiv2016

New insights in host-associated microbial diversity with broad and accurate taxonomic resolution

O_LIDeep microbiome profiling has sparked a revolution in biology, recontextualizing mechanisms such as macroorganismal adaptation and evolution. Amplicon sequencing has been critical for characterization of highly diverse microbiomes, but several challenges still hinder their investigation: (1) Poor coverage of the full diversity, (2) Read depth losses and (3) Erroneous diversity inflation/distortion.\nC_LIO_LIWe developed a modular approach to quickly profile at least 8 interchangeable loci in a single sequencing run, including a simple and cost-effective way to block amplification of non-targets (like host DNA). We further correct observed distortion in amplified diversity by phylogenetically grouping erroneous OTUs, creating a phylogeny-based unit we call OPUs.\nC_LIO_LIOur approach achieves full, accurate characterization of a mixed-kingdom mock community of bacteria, fungi and oomycetes at high depth even in non-target contaminated systems. The OPU concept enables much more accurate estimations of alpha and beta diversity trends than OTUs and overcomes disagreements between studies caused by methodology. Leveraging the approach in the Arabidopsis thaliana phyllosphere, we generated to our knowledge the most complete microbiome survey to date.\nC_LIO_LIMicrobiomes are extremely diverse, extending well beyond bacteria and fungi. Our method makes new questions in a variety of fields tractable with accurate, systems-based overviews of microbial community structures.\nC_LI

Microbiology↗

bioRxiv2016

The fitness burden imposed by synthesizing quorum sensing signals

It is now well established that bacterial populations utilize cell-to-cell signaling (quorum-sensing, QS) to control the production of public goods and other co-operative behaviours. Evolutionary theory predicts that both the cost of signal production and the response to signals should incur fitness costs for producing cells. Although costs imposed by the downstream consequences of QS have been shown, it has not been demonstrated that the production of QS signal molecules (QSSMs) results in a decrease in fitness. We measured the fitness cost to cells of synthesising QSSMs by quantifying metabolite levels in the presence of QSSM synthases. We found that: (i) bacteria making QSSMs have a growth defect that exerts an evolutionary cost, (ii) production of QSSMs correlates with reduced intracellular concentrations of QSSM precursors, (iii) the production of heterologous QSSMs negatively impacts the production of a native QSSM that shares common substrates, and (iv) supplementation with exogenously added metabolites partially rescued growth defects imposed by QSSM synthesis. These data provide the first direct experimental evidence that the production of QS signals carries fitness costs to producer cells.\n\nOriginality-Significance StatementBacterial cells within populations communicate with each other to control social behaviors by producing diffusible quorum sensing (QS) signal molecules. Evolutionary theory predicts that both the cost of signal production and the response to signals should incur fitness costs for producing cells. Here we provide the first empirical evidence that the production of QS signals incurs fitness costs to producing cells. Since QS plays a major role in bacterial pathogenicity, this finding will underpin novel antimicrobial strategies that are urgently needed to replace currently available antimicrobials that are becoming obsolete through the ever-rising incidence of resistance.

Microbiology↗

bioRxiv2016

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients

Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-CF bronchiectasis microbiome in sputum with respect to clinical variables.\n\nEighty-five patients with non-cystic fibrosis (CF) bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data.\n\nMicrobial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations.\n\nThe use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their microbiome, taking into account pathogen load, community stability, and acute and chronic community responses to antibiotics.

Microbiology↗

bioRxiv2016

Comparative analysis of protein evolution and RNA structural changes in the genome of pre-epidemic and epidemic Zika virus

Zika virus (ZIKV) infection is associated with microcephaly, neurological disorders and poor pregnancy outcome1-3 and no vaccine is available. Although ZIKV was first discovered in 1947, the exact mechanism of virus replication and pathogenesis still remains unknown. Recent outbreaks of Zika virus in the Americas clearly suggest a better adaptation of viral strains to human host. Understanding the conserved and adaptive features in the evolution of ZIKV genome will reveal the molecular mechanism of virus replication and host adaptation. Here, we show comprehensive analysis of protein evolution and changes in RNA secondary structures of ZIKV strains including the current 2015-16 outbreak. To identify the constraints on ZIKV evolution, selection pressure at individual codons, immune epitopes, co-evolving sites, and RNA structures were analyzed. The proteome of current 2015/16 epidemic ZIKV strains of Asian genotype is found to be genetically conserved due to genome-wide negative selection on codons, with limited positive selection. Predicted RNA structures at the 5 and 3 ends of ZIKV strains reveal substantial changes such as an additional stem loop which makes it similar to that of Yellow Fever Virus. Concisely, the targeted changes at both the amino acid and the RNA levels contribute to the better adaptation of ZIKV strains to human host with an enhanced neurotropism.

Microbiology↗

bioRxiv2016

Genetic and chemical differentiation of Campylobacter coli and Campylobacter jejuni lipooligosaccharide pathways

Despite the importance of lipooligosaccharides (LOS) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS in C. coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelated C. coli isolates sampled from several different host species. Furthermore, we paired C. coli genomic information and LOS chemical composition for the first time to identify mechanisms consistent with the generation of LOS phenotypic heterogeneity. After classifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structure heterogeneity. Mass spectrometry analysis of the LOS of nine isolates, representing four different LOS classes, identified two features distinguishing C. coli LOS from C. jejunis. GlcN-GlcN disaccharides were present in the lipid A backbone in contrast to the GlcN3N-GlcN backbone observed in C. jejuni. Moreover, despite that many of the genes putatively involved in Qui3pNAcyl were absence in the genomes of various isolates, this rare sugar was found in the outer core of all C. coli. Therefore, regardless the high genetic diversity of LOS biosynthes is locus in C. coli, we identified species-specific phenotypic features of C. coli LOS which might explain differences between C. jejuni and C. coli in terms of population dynamics and host adaptation.\n\nDepositories (where applicable)The whole genome sequences of C. coli are publicly available on the RAST server (http://rast.nmpdr.org) with guest account (login and password guest) under IDs: 195.91, 195.96-195.119, 195.124-195.126, 195.128-195.130, 195.133, 195.134, 6666666.94320

Microbiology↗

bioRxiv2016

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI)

Mass spectrometry imaging (MSI) has emerged as a powerful technique enabling spatially defined imaging of metabolites within microbial biofilms. Here, we extend this approach to enable differentiation of newly synthesized versus pre-existing metabolites across a co-culture. This is accomplished by MS imaging two soil microbes, Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2, that were administered heavy water (D2O) during growth on agar plates. For two species-specific diglyceride (DG) lipids, isotopic analysis was performed on each spectra collected across the co-culture to determine the relative amount of newly synthesized versus pre-existing lipid. Here, highest levels of new synthesis of RCH2 lipid was localized to border regions adjacent to S. oneidensis MR1, while the MR1 lipid showed highest levels in regions further from RCH2. Interestingly, regions of high lipid abundance did not correspond to the regions with highest new lipid biosynthesis. Given the simplicity and generality of using D2O as a stable isotopic probe combined with the accessibility of kMSI to a range of MSI instrumentation, this approach has broad application for improving our understanding of how microbial interactions influence metabolite biosynthesis.

Microbiology↗

bioRxiv2016

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites

Animal and plant richness in tropical rainforests has long intrigued naturalist. More recent work has revealed that parasites contribute to high tropical tree diversity (Bagchi et al., 2014; Terborgh, 2012) and that arthropods are the most diverse eukaryotes in these forests (Erwin, 1982; Basset et al., 2012). It is unknown if similar patterns are reflected at the microbial scale with unicellular eukaryotes or protists. Here we show, using environmental metabarcoding and a novel phylogeny-aware cleaning step, that protists inhabiting Neotropical rainforest soils are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific protist parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, we found too few Oomycota to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model (Janzen, 1970; Connell, 1970). Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that microbes play a large role in tropical terrestrial ecosystems long viewed as being dominated by macro-organisms.\n\nContact: dunthorn@rhrk.uni-kl.de

Microbiology↗

bioRxiv2016

Origin of modern syphilis and emergence of a contemporary pandemic cluster

Syphilis swept across the world in the 16th century as one of most prominent documented pandemics and is re-emerging worldwide despite the availability of effective antibiotics. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the non-cultivable and clonal nature of the causative bacterium Treponema pallidum subsp. pallidum. In this study, we used DNA capture and next generation sequencing to obtain whole genome data from syphilis patient specimens and from treponemes propagated in laboratory settings. Phylogenetic analyses indicate that the syphilis strains examined here share a common ancestor after the 15th century. Moreover, most contemporary strains are azithromycin resistant and members of a globally dominant cluster named here as SS14-{Omega}. This cluster diversified from a common ancestor in the mid-20th century and has the population genetic and epidemiological features indicative of the emergence of a pandemic strain cluster.

Microbiology↗

bioRxiv2016

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

BackgroundPost-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects.\n\nResultsWe utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal Na acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM.\n\nConclusionsUnbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints.

Microbiology↗

bioRxiv2016

Chloroquine inhibits Zika Virus infection in different cellular models

Zika virus (ZIKV) infection in utero might lead to microcephaly and other congenital defects. In adults, cases of Guillain-Barre syndrome and meningoencephalitis associated with ZIKV infection have been reported, and no specific therapy is available so far. There is urgency for the discovery of antiviral agents capable of inhibiting viral replication and its deleterious effects. Chloroquine is widely administered as an antimalarial drug, anti-inflammatory agent, and it also shows antiviral activity against several viruses. Here we show that chloroquine exhibits antiviral activity against ZIKV in VERO, human brain microvascular endothelial, and neural stem cells. We demonstrated in vitro that chloroquine reduces the number of ZIKV-infected cells, virus production and cell death promoted by ZIKV infection without cytotoxic effects. Our results suggest that chloroquine is a promising candidate for ZIKV clinical trials, since it is already approved for clinical use and can be safely administered to pregnant woman.

Microbiology↗

bioRxiv2016

P2Y2 purinergic receptor is induced following human cytomegalovirus infection and its activity is required for efficient viral replication

Human cytomegalovirus (HCMV) manipulates many aspects of host cell biology to create an intracellular milieu optimally supportive of its replication and spread. The current study reveals a role for purinergic signaling in HCMV infection. The levels of several components of the purinergic signaling system, including the P2Y2 receptor, were altered in HCMV-infected fibroblasts. P2Y2 receptor RNA and protein are strongly induced following infection. Pharmacological inhibition of receptor activity or knockdown of receptor expression markedly reduced the production of infectious HCMV progeny. When P2Y2 activity was inhibited, the accumulation of most viral RNAs tested and viral DNA was reduced. In addition, the level of cytosolic calcium within infected cells was reduced when P2Y2 signaling was blocked. The HCMV-coded UL37x1 protein was previously shown to induce calcium flux from the smooth endoplasmic reticulum to the cytosol, and the present study demonstrates that P2Y2 function is required for this mobilization. We conclude that P2Y2 supports the production of HCMV progeny, possibly at multiple points within the viral replication cycle that interface with signaling pathways induced by the purinergic receptor.\n\nImportanceHCMV infection is ubiquitous and can cause life-threatening disease in immunocompromised patients, debilitating birth defects in newborns, and has been increasingly associated with a wide range of chronic conditions. Such broad clinical implications result from the modulation of multiple host cell processes. This study documents that cellular purinergic signaling is usurped in HCMV-infected cells and that the function of this signaling axis is critical for efficient HCMV infection. Therefore, we speculate that blocking P2Y2 receptor activity has the potential to become an attractive novel treatment option for HCMV infection.

Microbiology↗