SEARCH · Search bioRxiv

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20Linked to original sources

bioRxiv2016

Minimal Tool Set for a Prokaryotic Circadian Clock

BackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.\n\nResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.\n\nConclusionOur analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.

Microbiology↗

bioRxiv2016

Antibiotic susceptibility of bacterial colonies: An assay and experiments with Staphylococcus aureus.

A method is presented to evaluate in vitro the efficacy of antibiotics to treat bacteria growing as discrete colonies on surfaces and the contribution of the colony structure to the antibiotic susceptibility of bacteria. Using this method, we explored the relative efficacy of six bactericidal and three bacteriostatic antibiotics to inhibit the growth and kill Staphylococcus aureus colonies of different sizes, densities and ages. As measured by the reduction in viable cell density relative to untreated controls, of the bactericidal drugs tested ciprofloxacin and gentamicin were most effective. By this criteria, ampicillin was more effective than oxacillin. Daptomycin and vancomycin were virtually ineffective for treating S. aureus growing as colonies. The bacteriostatic antibiotic tested, tetracycline, linezolid and erythromycin were all able to prevent the growth of S. aureus colonies and did so even more effectively than daptomycin, which is highly bactericidal in liquid culture. The results of these experiments and other observations suggest that relative inefficacy of oxacillin, vancomycin and daptomycin to kill S. aureus in colonies is due to the density and physiological state of the bacteria rather than the inability of these drugs to penetrate the colonies. The methods developed here are general and can be used to explore the efficacy of antibiotics to treat bacteria growing in biofilms as well as discrete colonies.

Microbiology↗

bioRxiv2016

Aerobic H2 respiration enhances metabolic flexibility of methanotrophic bacteria

Methanotrophic bacteria are important soil biofilters for the climate-active gas methane. The prevailing opinion is that these bacteria exclusively metabolise single-carbon, and in limited instances, short-chain hydrocarbons for growth. This specialist lifestyle juxtaposes metabolic flexibility, a key strategy for environmental adaptation of microorganisms. Here we show that a methanotrophic bacterium from the phylum Verrucomicrobia oxidises hydrogen gas (H2) during growth and persistence. Methylacidiphilum sp. RTK17.1 expresses a membrane-bound hydrogenase to aerobically respire molecular H2 at environmentally significant concentrations. While H2 oxidation did not support growth as the sole electron source, it significantly enhanced mixotrophic growth yields under both oxygen-replete and oxygen-limiting conditions and was sustained in non-growing cultures starved for methane. We propose that H2 is consumed by this bacterium for mixotrophic growth and persistence in a manner similar to other non-methanotrophic soil microorganisms. We have identified genes encoding oxygen-tolerant uptake hydrogenases in all publicly-available methanotroph genomes, suggesting that H2 oxidation serves a general strategy for methanotrophs to remain energised in chemically-limited environments.

Microbiology↗

bioRxiv2016

Comparison of African, Asian, and American Zika Viruses in Swiss Webster mice: Virulence, neutralizing antibodies, and serotypes

The sequence of Zika virus has evolved as it has spread out of Africa and into the Americas. It is unclear whether American strains of the virus define a new serotype. Here, we have tested the virulence and immunogenicity of three wild-type ZIKV strains in neonatal Swiss Webster mice. We found that all three ZIKV strains (African MR766, 1947; Asian FSS13025, 2010; and American, PRVABC59, 2015) are capable of killing neonatal mice after intracranial injection. Intraperitoneal injection with these viruses did not kill, but produced neutralizing antibodies as measured by a PRNT50 assay. Sera from mice infected with each virus were tested for neutralizing activity against the infecting virus and also the other two viruses by a PRNT50 assay. In general, the antibodies induced by each virus were good at neutralizing that virus (the homologous virus), but somewhat poorer at neutralizing the other two viruses (heterologous viruses). Antibodies induced by the African strain MR766 were about 4-fold worse at neutralizing the American strain PRVABC59 than the homologous strain, while antibodies induced by the American strain were about 10-fold worse at neutralizing the African strain than the homologous strain. Because the antibodies are cross-neutralizing at some level, the viruses do not form separate serotypes. Nevertheless, these results raise concern that the immunity conferred by the African virus may protect only relatively poorly against the new American strains. This has implications for the possible spread of the American ZIKV strains to Africa and Southeast Asia, and also for the development of vaccines.

Microbiology↗

bioRxiv2016

Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence

Streptococcus pneumoniae becomes competent for genetic transformation when exposed to an autoinducer peptide named CSP. This peptide was originally described as a quorum-sensing (QS) signal, enabling individual cells to regulate competence in response to population density. However, recent studies suggest that CSP may instead serve as a probe for sensing environmental cues, such as antibiotic stress or environmental diffusion. Here, we show that competence induction can be simultaneously influenced by cell density, external pH, antibiotic-induced stress and cell history. Our experimental data is explained by a mathematical model where the environment and cell history modify how cells produce or sense CSP. Taken together, model and experiments indicate that autoinducer concentration can function as an indicator of cell density across environmental conditions, while also incorporating information on environmental factors or cell history, allowing cells to integrate cues such as antibiotic stress into their QS response. This unifying perspective may apply to other debated QS systems.

Microbiology↗

bioRxiv2016

Nuclear pore-like structures in a compartmentalized bacterium

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immuno-gold labelling demonstrates localization of one such protein, containing a {beta}-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

Microbiology↗

bioRxiv2016

Parasitic Infection by Pseudocapillaria tomentosa is Associated with a Longitudinal Restructuring of the Zebrafish Gut Microbiome

Helminth parasites represent a significant threat to wild, domesticated, and research animal health. Pseudocapillaria tomentosa is a common intestinal nematode parasite and an important source of infection in zebrafish. Symptoms of the infection vary widely from no clinical signs to sever emaciation and mortality, however, the reasons underpinning these disparate outcomes are unclear. Components of the microbiome may interact with parasites to influence their success in the gut while parasite infections are also known to influence the composition of the gut microbiome. In this study we evaluated the longitudinal changes in the gut microbiome structure and gut physiology during experimental P. tomentosa infection in adult 5D line zebrafish. We observed less severe signs of infection and less mortality in these fish than previously described in AB line fish. However, inflammation and epithelial hyperplasia in the intestine was still observed in infected 5D line fish. The composition of the microbiome changed rapidly during the infection and these changes were associated with parasite stage of development and burden. Individual taxa covaried with parasite abundance in the intestine intimating the gut microbiome may influence parasite burden. Associations between taxa and parasite abundance in some cases appeared to be phylogenetically patterned. Strong positive associations were observed between OTUs phylotyped to Proteobacteria and abundance of adult parasites and parasite eggs. Together these experiments demonstrate that P. tomentosa infection results in a rapid and temporally dynamic disruption of the zebrafish gut microbiome and clarify how interactions between the gut microbiome and intestinal parasites may impact fish populations.

Microbiology↗

bioRxiv2016

Human Endometrial Stromal Cells Are Highly Permissive To Productive Infection by Zika Virus

Zika virus (ZIKV) is a recently re-emerged flavivirus transmitted to humans by mosquito bites but also from mother to fetus and by sexual intercourse. We here show for the first time that primary human endometrial stromal cells (HESC) are highly permissive to ZIKV infection and support its in vitro replication. ZIKV envelope expression was detected in the endoplasmic reticulum whereas double-stranded viral RNA colocalized with vimentin filaments to the perinuclear region. ZIKV productive infection also occurred in the human T-HESC cell line with the induction of interferon-{beta} (IFN-{beta}) and of IFN-stimulated genes. Notably, in vitro decidualization of T-HESC with cyclic AMP and progesterone upregulated the cell surface expression of the ZIKV entry co-receptor AXL and boosted ZIKV replication by ca. 100-fold. Thus, endometrial stromal cells, particularly if decidualized, likely represent a crucial cell target of sexual virus transmission and a relevant source of ZIKV spreading to placental trophoblasts during pregnancy.\n\nAUTHOR SUMMARYInfection by Zika virus (ZIKV), a flavivirus transmitted to humans by mosquito bites, has recently emerged as an important cause of neurological lesions in the fetal brain as women who become infected by ZIKV during pregnancy can transmit the virus to their fetus. In addition, routes of ZIKV transmission independent of mosquito bites have been also identified and include sexual transmission from both infected men and women to their partners, an aspect bearing great societal implications for ZIKV spread. These observations highlight the importance of the female reproductive tract in the establishment and/or spreading of the infection. In this regard, the endometrium is a highly dynamic tissue undergoing major histological changes during the menstrual cycle under the coordinated action of sexual hormones. In particular, progesterone drives the differentiation of human endometrial stromal cells towards decidualization, a process that is critical for fetal trophoblast invasion and placenta formation. We here report for the first time that both primary and immortalized human endometrial stromal cells are highly permissive to ZIKV infection and replication, particularly when in vitro decidualized by progesterone, suggesting that these cells could significantly contribute to vertical ZIKV transmission in utero during pregnancy but also to horizontal transmission by the sexual route.

Microbiology↗

bioRxiv2016

Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms

Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics in Pseudomonas aeruginosa biofilms. Irrespective of initial frequency, in competition with matrix mutants, wild type cells always increase in relative abundance in straight-tunnel microfluidic devices under simple flow regimes. By contrast, in microenvironments with complex, irregular flow profiles - which are common in natural environments - wild type matrix-producing and isogenic non-producing strains can coexist. This result stems from local obstruction of flow by wild-type matrix producers, which generates regions of near-zero flow speed that allow matrix mutants to locally accumulate. Our findings connect the evolutionary stability of matrix production with the hydrodynamics and spatial structure of the surrounding environment, providing a potential explanation for the variation in biofilm matrix secretion observed among bacteria in natural environments.\n\nImpact StatementThe feedback between hydrodynamic flow conditions and biofilm spatial architecture drives competition in P. aeruginosa biofilms, and can explain the variation in biofilm production observed among bacteria in natural environments.

Microbiology↗

bioRxiv2016

Origins and Global Context of Brucella abortus in Italy

BackgroundBrucellosis is a common and chronic disease of cattle and other bovids that often causes reproductive disorders. Natural infection in cattle is caused by Brucella abortus and transmission typically occurs during abortions, calving, or nursing. Brucellosis is also a major zoonotic disease due to contamination of dairy products or contact with the tissues of infected animals. Brucellosis has been eradicated from most of the developed world in the last forty years but persists in many regions; B. abortus remains prevalent in portions of Africa, the Middle East, Asia, and Central and South America, as well as in the Mediterranean basin. Specifically, B. abortus has persisted in southern Italy in both cattle and water buffalo. Previous attempts at analyzing the genetic structure of B. abortus in Italy have been challenging due to the limited genetic variability and unresolved global population structure of this pathogen.\n\nResultsWe conducted genome-wide phylogenetic analysis on 11 representative strains of B. abortus from Italy, and compared these sequences to a worldwide collection of publically available genomes. Italian isolates belong to three clades basal to the global B. abortus lineage. Using six assays designed to identify substructure within the Italian clades in a collection of 261 isolates, one clade predominates throughout endemic districts in the country, while the other two clades are more geographically restricted to southern Italy.\n\nConclusionsAlthough related strains exist worldwide, B. abortus isolates from Italy are substantially different than those found in much of the rest of Europe and North America, and are more closely related to strains from the Middle East and Asia. Our assays targeting genetic substructure within Italy allowed us to identify the major lineages quickly and inexpensively, without having to generate whole genome sequences for a large isolate collection. These findings highlight the importance of genetic studies to assess the status and the history of pathogens.

Microbiology↗

bioRxiv2016

Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division.

How bacteria produce a septum to divide in two is not well understood. This process is mediated by periplasmic cell-wall producing enzymes that are positioned by filaments of the cytoplasmic membrane-associated actin FtsA and the tubulin FtsZ (FtsAZ). To understand how these components act in concert to divide cells, we visualized their movements relative to the dynamics of cell wall synthesis during cytokinesis. We find that the division septum is built at discrete sites that move around the division plane. Furthermore, FtsAZ filaments treadmill in circumferential paths around the division ring, pulling along the associated cell-wall-synthesizing enzymes. We show that the rate of FtsZ treadmilling controls both the rate of cell wall synthesis and cell division. The coupling of both the position and activity of the cell wall synthases to FtsAZ treadmilling guides the progressive insertion of new cell wall, synthesizing increasingly small concentric rings to divide the cell.\n\nOne-sentence summaryBacterial cytokinesis is controlled by circumferential treadmilling of FtsAZ filaments that drives the insertion of new cell wall.

Microbiology↗

bioRxiv2016

GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis

The bacterial tubulin FtsZ is the central component of the division machinery, coordinating an ensemble of proteins involved in septal cell-wall synthesis to ensure successful constriction. How cells achieve this coordination is unknown. We used a combination of imaging, genetic and biochemical approaches to demonstrate that in Escherichia coli cells FtsZ exhibits dynamic treadmilling predominantly determined by its GTPase activity, and that the treadmilling dynamics directs processive movement of the septal cell-wall synthesis machinery. In FtsZ mutants with severely reduced treadmilling, the spatial distribution of septal synthesis and the molecular composition and ultrastructure of the septal cell wall are substantially altered. Thus, the treadmilling of FtsZ provides a novel and robust mechanism for achieving uniform septal cell-wall synthesis to enable correct new pole morphology.\n\nOne-sentence summaryThe bacterial tubulin FtsZ uses GTP hydrolysis to power treadmilling, driving processive synthesis of the septal cell wall.

Microbiology↗

bioRxiv2016

Evolutionary and Functional Implications of Hypervariable Loci Within the Skin Virome

Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and anti-microbial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers. HPV and Staphylococcus phages contained 106 and 465 regions of diversification, or hypervariable loci, respectively. Propionibacterium phage genomes were minimally divergent and contained no hypervariable loci. Genes containing hypervariable loci were involved in functions including host tropism and immune evasion. HPV and Staphylococcus phage hypervariable loci were associated with purifying selection. Amino acid substitution patterns were virus dependent, as were predictions of their phenotypic effects. We identified diversity generating retroelements as one likely mechanism driving hypervariability. We validated these findings in an independently collected skin metagenomic sequence dataset, suggesting that these features of skin virome genomic variability are widespread. Our results highlight the genomic variation landscape of the skin virome and provide a foundation for better understanding community viral evolution and the functional implications of genomic diversification of skin viruses.

Microbiology↗

bioRxiv2016

Rapid molecular detection of Zika virus in urine using the recombinase polymerase amplification assay

BackgroundCurrently the detection of Zika virus (ZIKV) in patient samples is done by real-time RT-PCR. Samples collected from rural area are sent to highly equipped laboratories for screening. A rapid point-of-care test is needed to detect the virus, especially at low resource settings.\n\nMethodology/Principal FindingsIn this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV. RT-RPA assay was portable, sensitive (21 RNA molecules), and rapid (3-15 minutes). No cross-reactivity was detected to other flaviviruses, alphaviruses and arboviruses. Compared to real-time RT-PCR, the diagnostic sensitivity was 92%, while the specificity was 100%.\n\nConclusions/SignificanceThe developed assay is a promising platform for rapid point of need detection of ZIKV in low resource settings and elsewhere (e.g. during mass gathering).\n\nAuthor SummaryCurrently, Dengue (DENV), Zika (ZIKV) and Chikungunya (CHIKV) viruses represent a global threat. The clinical picture of the acute febrile diseases caused by DENV, ZIKV and CHIKV is very similar, in addition, the same mosquito vector is involved in the transmission cycle. The differentiation between them is of great importance as supportive treatment differs and the identification of any of the three viruses prompts implementation of control measures to avoid spreading of an outbreak. We have developed an assay for the detection of ZIKV genome. The assay based on isothermal \"recombinase polymerase amplification\" assay, which was performed at one temperature (42{degrees}C). The result was obtained in maximum of 15 minutes. Moreover, the assay is easy to be implemented at low resource settings.

Microbiology↗

bioRxiv2016

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,844 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

Microbiology↗

bioRxiv2016

Growth-Altering Microbial Interactions Are Highly Sensitive to Environmental Context

Microbial interactions are ubiquitous in nature, and equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed highly dynamic and responsive to environmental context.

Microbiology↗

bioRxiv2016

Genomic plasticity and rapid host switching promote the evolution of generalism in the zoonotic pathogen Campylobacter

Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of niche specifying genes and the opportunity for host transition can interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.

Microbiology↗

bioRxiv2016

In vivo bioluminescent imaging reveals temporal and spatial dynamics of giardiasis

Giardia lamblia is the most prevalent protistan parasite, causing acute and chronic diarrheal disease in over one billion people worldwide. Vertebrate hosts ingest Giardia cysts from contaminated sources, and these cysts excyst in the gut to become motile trophozoites. Trophozoites colonize the small intestine by attaching to the intestinal villi and later differentiate into infectious cysts that are released into the environment, completing Giardias life cycle. Due to the limited accessibility of the gastrointestinal tract, our understanding of in in vivo temporal and spatial dynamics of giardiasis is largely inferred from parasite physiology in laboratory culture. Yet parasite growth under in vitro culture conditions may not mirror in vivo parasite physiology in the host. Here we develop bioluminescent imaging (BLI) methods to directly interrogate the temporal and spatial dynamics of giardiasis in mice, providing an improved animal model for the evaluation of anti-Giardia drugs. This non-invasive method of imaging giardiasis allows unprecedented and precise quantification of in vivo temporal and spatial patterns of infection. By infecting mice with parasites expressing constitutive or encystation-specific luciferase bioreporters, we show that parasite colonization of the gut is not uniform. Metabolically active parasites primarily colonize the proximal small intestine in \"hot spots\"--high density foci of infection that likely result in localized pathology to the gut epithelium. Using in vivo and ex vivo BLI of encystation-specific bioreporters, we show that encystation initiates shortly after inoculation and parasites encyst throughout the entire duration of infection. We also find that encystation is initiated in high density foci in the proximal small intestine, rather than the colon as has been previously assumed, and show that the initiation of encystation is magnified in parasites incubated at high density in laboratory culture. Prior models have suggested that chemical cues cause parasites to encyst as they are dislodged from the upper gut and travel to more distal regions of the gastrointestinal tract. We suggest a model of encystation in which parasites reach a threshold density that results the induction of encystation due to local nutrient depletion. The in vivo imaging of giardiasis has redefined the dynamics of the Giardia life cycle in the host, paving the way for future mechanistic studies of density-dependent processes in this highly prevalent, yet understudied parasite.

Microbiology↗