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At least 307 records · Page 17Linked to original sources

bioRxiv2016

The clinically approved antiviral drug sofosbuvir impairs Brazilian zika virus replication

Zika virus (ZIKV) is a member of Flaviviridae family, as other agents of clinical significance, such as dengue (DENV) and hepatitis C (HCV) viruses. ZIKV spread from Africa to Pacific and South American territories, emerging as an etiological pathogen of neurological disorders, during fetal development and in adulthood. Therefore, antiviral drugs able to inhibit ZIKV replication are necessary. Broad spectrum antivirals, such as interferon, ribavirin and favipiravir, are harmful for pregnant animal models and women. The clinically approved uridine nucleotide analog anti-HCV drug, sofosbuvir, has not been affiliated to teratogenicity. Sofosbuvir target the most conserved protein over the members of the Flaviviridae family, the viral RNA polymerase. We thus studied ZIKV susceptibility to sofosbovir. We initially characterized a Brazilian ZIKV strain for use in experimental assays. Sofosbuvir inhibits the Brazilian ZIKV replication in a dose-dependent manner, both in BHK-21 cells and SH-Sy5y, by targeting ZIKV RNA polymerase activity, with the involvement of conserved amino acid residues over the members of Flaviviridae family. The identification of clinically approved antiviral drugs endowed with anti-ZIKV could reduce the time frame in pre-clinical development. Altogether, our data indicates that sofosbuvir chemical structure is endowed with anti-ZIKV activity.

Microbiology↗

bioRxiv2016

Influenza C incidence and herd immunity in Lancaster, UK, in the winter of 2014-2015

Influenza C is not included in the annual seasonal influenza vaccine, and has historically been regarded as a minor respiratory pathogen. However, recent work has highlighted its potential role as a cause of pneumonia in infants. We performed nasopharyngeal or nasal swabbing and/or serum sampling (n=148) in Lancaster, UK, over the winter of 2014-2015. Using enzyme-linked immunosorbent assay (ELISA), we estimated a seropositivity of 77%. By contrast, only 2 individuals, both asymptomatic adults, were influenza C-positive by polymerase chain reaction (PCR). Deep sequencing of nasopharyngeal samples produced partial sequences for 4 genome segments in one of these patients. Bayesian phylogenetic analysis demonstrated that the influenza C genome from this individual is evolutionarily distant to those sampled in recent years and represents a novel genome constellation, indicating that it is a product of a decades-old reassortment event. Although we find no evidence that influenza C was a significant respiratory pathogen during the winter of 2014-2015 in Lancaster, we confirm previous observations of seropositivity in the majority of the population. We calculate that this level of herd immunity would be sufficient to suppress epidemics of influenza C and restricts the virus to sporadic endemic spread.

microbiology↗

bioRxiv2016

Dysregulation of Long Non-coding RNA (lncRNA) Genes and Predicted lncRNA-protein Interactions during Zika Virus Infection

Zika Virus (ZIKV) is a causative agent for poor pregnancy outcome and fetal developmental abnormalities, including microcephaly and eye defects. As a result, ZIKV is now a confirmed teratogen. Understanding host-pathogen interactions, specifically cellular perturbations caused by ZIKV, can provide novel therapeutic targets. In order to complete viral replication, viral pathogens control the host cellular machineries and regulate various factors, including long noncoding RNA (lncRNA) genes, at transcriptional levels. The role of lncRNA genes in the pathogenesis of ZIKV-mediated microcephaly and eye defects is currently unknown. To gain additional insights, we focused on profiling the differentially expressed lncRNA genes during ZIKV infection in mammalian cells. For this study, we employed a contemporary clinical Zika viral isolate, PRVABC59, of Asian genotype. We utilized an unbiased RNA sequencing approach to profile the lncRNA transcriptome in ZIKV infected Vero cells. We identified a total of 121 lncRNA genes that are differentially regulated at 48 hours post-infection. The majority of these genes are independently validated by reverse-transcription qPCR. A notable observation was that the lncRNAs, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and NEAT1 (Nuclear Paraspeckle Assembly Transcript 1), are down-regulated upon Zika viral infection. MALAT1 and NEAT1 are known as nuclear localized RNAs that regulate gene expression and cell proliferation. Protein-lncRNA interaction maps revealed that MALAT1 and NEAT1 share common interacting partners and form a larger network comprising of 71 cellular factors. ZIKV-mediated dysregulation of these two regulatory lncRNAs can alter the expression of respective target genes and associated biological functions, an important one being cell division. In conclusion, this investigation is the first to provide insight into the biological connection of lncRNAs and ZIKV which can be further explored for developing antiviral therapy and understanding fetal developmental processes.

Microbiology↗

bioRxiv2016

Characterization of the effects of n-butanol on the cell envelope of E. coli

Biofuel alcohols have severe consequences on the microbial hosts used in their biosynthesis, which limits the productivity of the bioconversion. The cell envelope is one of the most strongly affected structures, in particular, as the external concentration of biofuels rises during biosynthesis. Damage to the cell envelope can have severe consequences, such as impairment of transport into and out of the cell; however the nature of butanol-induced envelope damage has not been well characterized. In the present study, the effects of n-butanol on the cell envelope of Escherichia coli were investigated. Using enzyme and fluorescence-based assays, we observed that 1% v/v n-butanol resulted in release of lipopolysaccharides from the outer membrane of E. coli and caused leakiness in both outer and inner membranes. Higher concentrations of n-butanol, within the range of 2% - 10% (v/v), resulted in inner membrane protrusion through the peptidoglycan observed by characteristic blebs. The findings suggest that strategies for rational engineering of butanol-tolerant bacterial strains should take into account all components of the cell envelope.

Microbiology↗

bioRxiv2016

Origins of pandemic clones from environmental gene pools

Some microbes can transition from an environmental lifestyle to a pathogenic one1-3. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes4,5. However, the genomic features that must be present in a population prior to the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, using Vibrio cholerae as a model. We then characterized several environmental VAP alleles to show that, while some of them reduced the ability of clinical strains to colonize a mammalian host, other alleles conferred efficient host colonization. These results show that VAPs are present in environmental bacterial populations prior to the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment, they become selected and enriched under certain ecologicalconditions, and finally a genomic background containing several VAPs acquires virulence factors that allows for its emergence as a pathogenic clone.

Microbiology↗

bioRxiv2016

Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain

Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Kochs postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

Microbiology↗

bioRxiv2016

Benzoate and Salicylate Tolerant Strains Lose Antibiotic Resistance during Laboratory Evolution of Escherichia coli K-12

Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted experimental evolution by daily diluting cultures in increasing concentrations of benzoic acid (up to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from evolving populations showed increasing tolerance to benzoate but were sensitive to chloramphenicol and tetracycline. Sixteen clones grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth occurred in 10 mM salicylate. Benzoate-evolved strains grew like W3110 in the absence of benzoate; in media buffered at pH 4.8, pH 7.0, or pH 9.0; or in 20 mM acetate or sorbate at pH 6.5. Genomes of 16 strains revealed over 100 mutations including SNPs, large deletions, and insertion knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or in associated regulators such as rob and cpxA, as well as MDR efflux pumps emrA, emrY, and mdtA. Strains also lost or down-regulated the Gad acid fitness regulon. In 5 mM benzoate, or in 2 mM salicylate (2-hydroxybenzoate), most strains showed increased sensitivity to the antibiotics chloramphenicol and tetracycline; some strains were more sensitive than a marA knockout. Thus, our benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate or salicylate selection pressure may cause general loss of MDR genes and regulators.\n\nIMPORTANCEBenzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance. Similar aspirin-associated loss of drug resistance might occur in bacterial pathogens found in arterial plaques.

Microbiology↗

bioRxiv2016

Microbial Mat Functional and Compositional Sensitivity to Environmental Disturbance

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the activity of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. While this ecosystem undergoes a range of seasonal variation, it experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and activity of abundant and rare taxa, suggesting overall functional and compositional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low activity across conditions, the total number of active taxa and overall activity increased postdisturbance, with significant shifts in activity occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and activity. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.

Microbiology↗

bioRxiv2016

Comparative phylogenetic analysis of bacterial associates in Pyrrhocoroidea and evidence for ancient and persistent environmental symbiont reacquisition in Largidae (Hemiptera: Heteroptera).

The ancient insect order Hemiptera, one of the most well-studied insect lineages with respect to bacterial symbioses, still contains major branches which lack robust phylogenies and comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species]; Pyrrhocoridae [~300 species]) is a superfamily of the primarily-herbivorous hemipteran infraorder Pentatomomorpha, though relationships to related superfamilies are controversial. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes between these putative sister families. We surveyed bacterial diversity of this group using paired-end Illumina and targeted Sanger sequencing of bacterial 16S amplicons of 30 pyrrhocoroid taxa, including 17 species of Largidae, in order to determine the identity of bacterial associates and similarity of associated microbial communities among species. We also constructed the first comprehensive phylogeny of this superfamily (4,800 bp; 5 loci; 57 ingroup + 12 outgroup taxa) in order accurately trace the evolution of symbiotic complexes among Pentatomomorpha. We undertook multiple lines of investigation (i.e., experimental rearing, FISH microscopy, phylogenetic and co-evolutionary analyses) to understand potential transmission routes of largid symbionts. We found a prevalent, specific association of Largidae with plant-beneficial-environmental clade Burkholderia housed in midgut tubules. As in other distantly-related Heteroptera, symbiotic bacteria seem to be acquired from the environment every generation. We review current understanding of symbiotic complexes within the Pentatomomorpha and discuss means to further investigations of the evolution and function of these symbioses.\n\nImportanceObligate symbioses with bacteria are common in insects, particularly for Hemiptera wherein varied forms of symbiosis occur, though knowledge of symbionts remains incomplete for major lineages. Thus, an accurate understanding of how these partnerships evolved and changed over millions of years is not yet achievable. We contribute to our understanding of the evolution of symbiotic complexes in Hemiptera by characterizing bacterial associates of Pyrrhocoroidea focusing on the family Largidae and by constructing a phylogeny to establish evolutionary relationships of and within this group. Members of Largidae are associated with specific symbiotic Burkholderia from a different clade than Burkholderia symbionts in other Hemiptera and are members of the earliest-diverging superfamily of Burkholderia-associated Hemiptera. Evidence suggests that species of Largidae reacquire specific symbiotic bacteria every generation environmentally, a rare strategy for insects with potentially volatile evolutionary ramifications, but one that has persisted in Largidae and other related lineages since the Cretaceous.

Microbiology↗

bioRxiv2016

Tuberculosis susceptibility and vaccine protection are independently controlled by host genotype

The outcome of Mycobacterium tuberculosis (Mtb) infection and the immunological response to the Bacille Calmette Guerin (BCG) vaccine are highly variable in humans. Deciphering the relative importance of host genetics, environment, and vaccine preparation on BCG efficacy has proven difficult in natural populations. We developed a model system that captures the breadth of immunological responses observed in outbred individuals, which can be used to understand the contribution of host genetics to vaccine efficacy. This system employs a panel of highly-diverse inbred mouse strains, consisting of the founders and recombinant progeny of the \"Collaborative Cross\". Unlike natural populations, the structure of this panel allows the serial evaluation of genetically-identical individuals and quantification of genotype-specific effects of interventions such as vaccination. When analyzed in the aggregate, our panel resembled natural populations in several important respects; the animals displayed a broad range of Mtb susceptibility, varied in their immunological response to infection, and were not durably protected by BCG vaccination. However, when analyzed at the genotype level, we found that these phenotypic differences were heritable. Mtb susceptibility varied between lines, from extreme sensitivity to progressive Mtb clearance. Similarly, only a minority of the genotypes was protected by vaccination. BCG efficacy was genetically separable from susceptibility, and the lack of efficacy in the aggregate analysis was driven by nonresponsive lines that mounted a qualitatively distinct response to infection. These observations support an important role for host genetic diversity in determining BCG efficacy, and provide a new resource to rationally develop more broadly efficacious vaccines.\n\nImportance: Tuberculosis (TB) remains an urgent global health crisis, and the efficacy of the currently used TB vaccine, M. bovis BCG, is highly variable. The design of more broadly-efficacious vaccines depends on understanding the factors that limit the protection imparted by BCG. While these complex factors are difficult to disentangle in natural populations, we used a model population of mice to understand the role of host genetic composition to BCG efficacy. We found that the ability of BCG to protect an individual genotype was remarkably variable. BCG efficacy did not depend on the intrinsic susceptibility of the animal, but instead correlated with qualitative differences in the immune response to the pathogen. These studies suggest that host genetic polymorphism is a critical determinant of vaccine efficacy and provides a model system to develop interventions that will be useful in genetically diverse populations.

Microbiology↗

bioRxiv2016

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls, and different types of beads for bead-beating facilitating cell lysis. We evaluate DNA concentration, purity, and stability, and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead-beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate compared to standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from: https://dx.doi.org/10.6084/m9.figshare.3475406.\n\nIMPORTANCESequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial world associate with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources, and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism- (pathogen-) independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduction of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.

Microbiology↗

bioRxiv2016

MICROWAVE MUTAGENESIS OF BREVIBACILLUS PARABREVIS FOR ENHANCED CELLULASE PRODUCTION, AND INVESTIGATION ON THERMOSTABILITY OF THIS CELLULASE

Microwave mutagenesis of Brevibacillus parabrevis for enhanced cellulase production was attempted. Though microwave treatment could alter the cellulase activity of the test bacterium, none of the mutants obtained were found to be genetically stable, indicating the reversible nature of microwave-induced mutation(s). Thermal stability of the B. parabrevis cellulase was also investigated. This enzyme was found to be capable of retaining its activity even after heat treatment (50-121{degrees}C, for 30-60 min). Fluorescence spectrum revealed a red shift in the emission maxima of the heat-treated enzyme preparations, indicating some structural change upon heating, but no major loss of activity was observed. This enzyme was found to be active over a broad temp range, with 90{degrees}C as the optimum temp, which is interesting as the producing organism is a mesophile.

Microbiology↗

bioRxiv2016

Bacterial invasion of the pancreas revealed after analyses of the pancreatic cyst fluids

The involvement of bacterial translocation (BT) in the promotion of carcinogenesis has gained a considerable attention in the last years. At this point however BT has not been studied in the context of pancreatic cystic lesions and their development into pancreatic ductal adenocarcinoma. The aim of the study was to analyze if bacteria are present in pancreatic cyst fluid (PCF) collected from patients with suspected pancreatic cysts. Total DNA was isolated from sixty nine PCF. The occurrence of bacteria in PCF was analyzed using bacterial 16S rRNA gene-specific PCR-based method followed by sequence identification and quantitative PCR assay tuned up to different pathogenic and commensal human bacteria. Forty-seven out of sixty-nine samples (68%) were found positive for harboring bacterial 16S rRNA gene. Follow up sequencing analyses of the PCR products revealed that bacterial species related to Fusobacterium spp., Bacteroides spp., and Bacillus spp. were predominating the PCF samples. The results suggest that specific bacteria can translocate to the pancreas and become detectable in the PCF.

Microbiology↗

bioRxiv2016

S2 from Equine infectious anemia virus is an infectivity factor which counteracts the retroviral inhibitors SERINC5 and SERINC3

The lentivirus equine infectious anemia virus (EIAV) encodes S2, a pathogenic determinant important for virus replication and disease progression in horses. No molecular function has yet been linked to this accessory protein. We now report that S2 can replace the activity of Nef on HIV-1 infectivity, being required to antagonize the inhibitory activity of SERINC proteins on Nef-defective HIV-1. Similar to Nef, S2 excludes SERINC5 from virus particles and requires an ExxxLL motif predicted to recruit the clathrin adaptor AP2. Accordingly, a functional endocytic machinery is essential for S2-mediated infectivity enhancement, which is impaired by inhibitors of clathrin-mediated endocytosis. In addition to retargeting SERINC5 to a late endosomal compartment, S2 promotes the host factor degradation. Emphasizing the similarity with Nef, we show that S2 is myristoylated and, compatible with a crucial role of the post-translational modification, its N-terminal glycine is required for the anti-SERINC5 activity.\n\nEIAV-derived vectors devoid of S2 are less susceptible than HIV-1 to the inhibitory effect of both human and equine SERINC5. We then identified the envelope glycoprotein of EIAV as a determinant which also modulates retrovirus susceptibility to SERINC5, indicating a bi-modular ability of the equine lentivirus to counteract the host factor.\n\nS2 shares no sequence homology with other retroviral factors known to counteract SERINC5. Adding to primate lentivirus Nef and gammaretrovirus glycoGag, the accessory protein from EIAV makes another example of a retroviral virulence determinant which independently evolved SERINC5-antagonizing activity. SERINC5 therefore plays a critical role for the interaction of the host with diverse retrovirus pathogens.\n\nSignificance StatementSERINC5 and SERINC3 are recently discovered cellular inhibitors of retroviruses, which are incorporated into virus particles and impair their ability to propagate the infection to target cells. Only two groups of viruses (represented by HIV-1 and MLV) have so far been identified to have evolved the ability of counteracting SERINC inhibition. We now discovered that Equine infectious anemia virus, which causes a debilitating disease in horses, also acquired the ability to protect the virus particle from inhibition by SERINC5 and SERINC3, using its small protein S2. The evidence that three different retroviruses have independently evolved the ability to elude inhibition bySERINC5 and SERINC3 indicates that these cellular factors play a fundamental role against various retrovirus pathogens.

Microbiology↗

bioRxiv2016

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Microbiology↗

bioRxiv2016

A Novel Family of Genomics Islands Across Multiple Species of Streptococcus

The genus Streptococcus is one of the most genomically diverse and important human and agricultural pathogens. The acquisition of genomic islands (GIs) plays a central role in adaptation to new hosts in the genus pathogens. The research presented here employs a comparative genomics approach to define a novel family of GIs in the genus Streptococcus which also appears across strains of the same species. Specifically, we identified 9 Streptococcus genomes out of 67 sequenced genomes analyzed, and we termed these as 15bp Streptococcus genomic islands, or 15SGIs, including i) insertion adjacent to the 3 end of ribosome l7/l12 gene, ii) large inserts of horizontally acquired DNA, and iii) the presence of mobility genes (integrase) and replication initiators. We have identified a novel family of 15SGIs and seems to be important in species differentiation and adaptation to new hosts. It plays an important role during strain evolution in the genus Streptococcus.

Microbiology↗

bioRxiv2016

Microbial Communities are Well Adapted to Disturbances in Energy Input

Although microbial systems are well-suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20 day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function was used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appear inherently well-adapted to disturbances in energy input and that changes in community structure in both treatments are more dependent on internal dynamics than on external forcing. Results also show that the rare biosphere is critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, endogenous feedbacks were more important than exogenous drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics.\n\nIMPORTANCEWithin the broader ecological context, biological communities are often viewed as stable and only experience succession or replacement when subject to external perturbations, such as changes in food availability or introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic \"unstable\" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.

Microbiology↗

bioRxiv2016

Sequence based prediction of novel domains in the cellulosome of Ruminiclostridium thermocellum

Ruminiclostridium thermocellum strain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach of in silico analysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study.\n\nNoteThis research was conducted in 2014 for Clostridium thermocellum ATCC 27405. The bacterium was later reannotated as Ruminiclostridium thermocellum. See NCBI nonredundant RefSeq protein annotation details at http://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/reannotation/. The study utilizes Pfam-B database, which was discontinued with effect from release 28.0 (5/2015). Availability of new information, reannotation/modification in accession numbers might impact some of the analyzed values although effort has been made to provide latest accession numbers and reference strain parameters. The preprint version may contain grammatical and proofreading mistakes. Errors and omissions excepted.

Microbiology↗