Top 10 Biorxiv Papers Today in Microbiology


2.026 Mikeys
#1. Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia
Tamieka A Fraser, Mikaela G Bell, Patrick N.A Harris, Scott C Bell, Haakon Bergh, Thuy-Khanh Nguyen, Timothy J Kidd, Graeme R Nimmo, Derek S Sarovich, Erin P Price
Stenotrophomonas maltophilia is emerging as an important cause of disease in nosocomial and community-acquired settings, including bloodstream, wound and catheter-associated infections. Cystic fibrosis airways also provide optimal growth conditions for various opportunistic pathogens with high antibiotic tolerance, including S. maltophilia . Currently, there is no rapid, cost-effective, and accurate molecular method for detecting this potentially life-threatening pathogen, particularly in polymicrobial specimens, suggesting that its true prevalence may be underestimated. Here, we used large-scale comparative genomics to identify a specific genetic target for S. maltophilia , with subsequent development and validation of a real-time PCR assay for its detection. Analysis of 165 Stenotrophomonas spp. genomes identified a 4kb region specific to S. maltophilia , which was targeted for Black Hole Quencher assay design. Our assay yielded the positive detection of 89 of 89 (100%) clinical S. maltophilia strains, and no amplification of 23...
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biorxivpreprint: Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia https://t.co/QYQXWok6hG #bioRxiv
biorxiv_micrbio: Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia https://t.co/w1OvMVNOsU #biorxiv_micrbio
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Sample Sizes : [132, 4, 3, 4, 2, 2, 9, 8, 8, 4, 2, 11, 2, 11, 2, 4, 2]
Authors: 10
Total Words: 7106
Unqiue Words: 2795

2.023 Mikeys
#2. Resolution and co-occurrence patterns of Gardnerella leopoldii, Gardnerella swidsinskii, Gardnerella piotii and Gardnerella vaginalis within the vaginal microbiome
Janet E Hill, Arianne Albert
Gardnerella vaginalis a hallmark of vaginal dysbiosis, but is found in the microbiomes of women with and without vaginal symptoms. G. vaginalis encompasses diverse taxa differing in attributes that are potentially important for virulence, and there is evidence that 'clades' or 'subgroups' within the species are differentially associated with clinical outcomes. The G. vaginalis species description was recently emended, and three new species within the genus were defined ( leopoldii, swidsinskii, piotii ). 16S rRNA sequences for the four Gardnerella species are all >98.5% identical and no signature sequences differentiate them. We demonstrated that Gardnerella species can be resolved using partial chaperonin-60 (cpn60) sequences, with pairwise percent identities of 87.1-97.8% among the type strains. Pairwise co-occurrence patterns of Gardnerella spp. in the vaginal microbiomes of 413 reproductive aged Canadian women were investigated, and several significant co-occurrences of species were identified. Abundance of G. vaginalis , and...
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biorxivpreprint: Resolution and co-occurrence patterns of Gardnerella leopoldii, Gardnerella swidsinskii, Gardnerella piotii and Gardnerella vaginalis within the vaginal microbiome https://t.co/dtKFer2KZv #bioRxiv
biorxiv_micrbio: Resolution and co-occurrence patterns of Gardnerella leopoldii, Gardnerella swidsinskii, Gardnerella piotii and Gardnerella ... https://t.co/YKITOaOW6y #biorxiv_micrbio
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Authors: 2
Total Words: 0
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2.013 Mikeys
#3. Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle
Brooke A Clemmons, Cameron Martino, Joshua B Powers, Shawn Campagna, Brynn H Voy, Dallas R Donohoe, James Gaffney, Mallory M Embree, Phillip R Myer
The rumen microbiome is critical in ruminant nutrition and contributes to nutrient utilization and feed efficiency in cattle. Therefore, the objective of this study was to interrogate microbial and biochemical factors affecting divergences in feed efficiency in Angus steers using 16S amplicon sequencing and untargeted metabolomics. Average residual feed intake (RFI) was calculated, and steers were divided into low- and high-RFI groups. Features were ranked in relation to RFI through supervised machine learning on microbial and metabolite compositions. Residual feed intake was associated with several attributes of the rumen bacterial community. Low-RFI steers were associated with decreased bacterial α- (P=0.03) and β- diversity (P<0.001). Several serum metabolites were associated with RFI. Based on fold change (high/low RFI), low-RFI steers had greater abundances of pantothenate (P=0.02). Machine learning on RFI was predictive of both serum metabolomic signature and rumen bacterial composition (AUC ≥0.7). Log-ratio proportions of...
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biorxivpreprint: Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle https://t.co/ex7JUqpmHy #bioRxiv
biorxiv_micrbio: Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle https://t.co/NhdH42Ooxc #biorxiv_micrbio
sbotlite: RT @biorxivpreprint: Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle https://t.co/ex7JUqpmHy…
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Authors: 9
Total Words: 0
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1.998 Mikeys
#4. Insulin potentiates JAK/STAT signaling to broadly inhibit flavivirus replication in insect vectors
Laura R.H. Ahlers, Chasity E. Trammell, Grace F. Carrell, Sophie Mackinnon, Brandi K. Torrevillas, Clement Y. Chow, Shirley Luckhart, Alan G. Goodman
The World Health Organization estimates that over half of the world's population is at risk for vector-borne diseases, such as those caused by arboviral infection. Because many arboviruses are mosquito-borne, investigation of the insect immune response will help identify targets that could reduce the spread of these viruses by the mosquito. In this study, we used a genetic screening approach to identify insulin-like receptor as a novel component of the immune response to arboviral infection. We determined that vertebrate insulin reduces West Nile virus (WNV) replication in Drosophila melanogaster as well as WNV, Zika, and dengue virus titers in mosquito cells. Mechanistically, we showed that insulin signaling activates the JAK/STAT, but not RNAi, pathway to control infection. Finally, we validated that insulin priming of adult female Culex mosquitoes through a blood meal reduces WNV infection, demonstrating an essential role for insulin signaling in insect antiviral responses to emerging human pathogens.
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biorxivpreprint: Insulin potentiates JAK/STAT signaling to broadly inhibit flavivirus replication in insect vectors https://t.co/Lh8BkoZD1r #bioRxiv
biorxiv_micrbio: Insulin potentiates JAK/STAT signaling to broadly inhibit flavivirus replication in insect vectors https://t.co/DqguhmRBR3 #biorxiv_micrbio
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Authors: 8
Total Words: 0
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1.998 Mikeys
#5. Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain
Syun-suke Kadoya, Syun-ichi Urayama, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Masaaki Kitajima, Toyoko Nakagomi, Osamu Nakagomi, Satoshi Okabe, Osamu Nishimura, Daisuke Sano
RNA viruses form a dynamic distribution of mutant swarm (termed 'quasispecies') due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect in that only part of a viral population can reach the next susceptible hosts. In the present study, the rhesus rotavirus (RRV) strain of Rotavirus A was serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001 in duplicate (the 1st and 2nd lineages), and three phenotypes (infectious titer, cell binding ability and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial...
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biorxivpreprint: Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain https://t.co/KIEbfWFa2L #bioRxiv
biorxiv_micrbio: Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain https://t.co/j5Upzkrcq8 #biorxiv_micrbio
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Authors: 11
Total Words: 10206
Unqiue Words: 3220

1.998 Mikeys
#6. Inhibiting HIV-1 and MMLV Reverse Transcriptase: The potential of an Allosteric Broad-Spectrum Inhibitor
Kwok Fong Chan, Ser Xian Phua, Chinh Tran To Su, Samuel KE Gan
Since drug resistance mutations in HIV-1 have been increasingly reported to resist most of the current drug repertoire in the antiretroviral therapy, there is a demand for new drugs. In this study, we focused on the viral enzyme Reverse Transcriptase (RT) as it is a good drug target given its absence in non-viruses. Through a reverse transcription assay screen, we found two out of forty compounds from the NCI Diversity Set V to inhibit HIV-1 RT activity. The less potent compound also inhibited MMLV RT. Molecular docking, structural conservation and binding pocket analyses suggested similar binding mechanisms of the dual inhibitor to the targets, implying that the phenylbenzoic scaffold may be potentially used to design broad-spectrum inhibitors against multiple Reverse Transcriptase enzymes from multiple viruses.
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biorxivpreprint: Inhibiting HIV-1 and MMLV Reverse Transcriptase: The potential of an Allosteric Broad-Spectrum Inhibitor https://t.co/akSKdqOc0w #bioRxiv
biorxiv_micrbio: Inhibiting HIV-1 and MMLV Reverse Transcriptase: The potential of an Allosteric Broad-Spectrum Inhibitor https://t.co/NMGYmaG9a7 #biorxiv_micrbio
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Authors: 4
Total Words: 5122
Unqiue Words: 1772

1.998 Mikeys
#7. Investigating the influence of spore maturation and sporulation conditions on MalS expression during Bacillus subtilis spore germination.
Bhagyashree Swarge, Chahida Nafid, Norbert Fischer, Stanley Brul
Spore forming bacteria of the orders Bacillales and Clostridiales play a major role in food spoilage and food-borne diseases. The spores remain in a dormant state for extended periods due to their highly resistant features. When environmental conditions become favourable, they can germinate as the germinant receptors located on the spores' inner membrane get activated via germinant binding. This leads to the formation of vegetative cells via germination and subsequent outgrowth. The present study focuses on the synthesis of protein MalS during B. subtilis spore germination by investigating the dynamics of the fluorescence level of a MalS-GFP fusion protein using time-lapse fluorescence microscopy. Our results show an initial increase within the first 15 minutes of germination, followed by a drop and stabilization of the fluorescence throughout the spore ripening period. Western blot analyses, however, indicate no increase in the levels of the MalS-GFP fusion protein during the first 15 minutes after the addition of the germinants....
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Authors: 4
Total Words: 5421
Unqiue Words: 1642

1.998 Mikeys
#8. Prevalence of Chlamydia trachomatis and Candida albicans; hospital based study
Albert Njeru, Joseph Mwafaida
Background: Chlamydia and candidiasis have only mild or no symptoms at all. When symptoms develop, they are often mistaken for something else like urinary tract infections or yeast infections. These infections affect both men and woman of all backgrounds and economic levels. Objective: The prevalence of Chlamydia trachomatis (C. trachomatis) and Candida albicans (C. albicans) infections among attendees of Kilifi Medical Centre in Kilifi county , Kenya was studied. Methodology: Urethral and vaginal swabs samples were aseptically collected from 305 subjects, examined for Candida albicans and Chlamydia trachomatis using standard microbiological methods. The swabs were analyzed using direct wet smears, Gram-stained smear and culture techniques. Results: Of the 305 participants, 181 (59.34%) females and 124 (40.66%) males were tested with the overall prevalence of 53.44 % for both Chlamydia trachomatis and Candida albicans with females having a higher infection rate (35.14 %) for chlamydia and candidasis than men (17.71). Amongst the...
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microh_dtu: RT @biorxiv_micrbio: Prevalence of Chlamydia trachomatis and Candida albicans; hospital based study https://t.co/jCt91pppPK #biorxiv_micrb…
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Total Words: 0
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1.998 Mikeys
#9. Restoration of wild-type motility to flagellin-knockout Escherichia coli
Nicholas Maitland Thomson, Mark John Pallen
Flagellin is the major constituent of the flagellar filament and faithful restoration of wild-type motility to flagellin mutants may be beneficial for studies of flagellar biology and biotechnological exploitation of the flagellar system. Therefore, we explored the restoration of motility by flagellin expressed from a variety of combinations of promoter, plasmid copy number and induction strength. Motility was only partially restored using the tightly regulated rhamnose promoter, but wild-type motility was achieved with the T5 promoter, which, although leaky, allowed titration of induction strength. Motility was little affected by plasmid copy number when dependent on inducible promoters. However, plasmid copy number was important when expression was controlled by the native E. coli flagellin promoter. Motility was poorly correlated with flagellin transcription levels, but strongly correlated with the amount of flagellin associated with the flagellar filament, suggesting that excess monomers are either not exported or not...
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biorxivpreprint: Restoration of wild-type motility to flagellin-knockout Escherichia coli https://t.co/vSWzC4kmAI #bioRxiv
biorxiv_micrbio: Restoration of wild-type motility to flagellin-knockout Escherichia coli https://t.co/HOzO3lGT6s #biorxiv_micrbio
surt_lab: RT @biorxivpreprint: Restoration of wild-type motility to flagellin-knockout Escherichia coli https://t.co/vSWzC4kmAI #bioRxiv
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Authors: 2
Total Words: 6019
Unqiue Words: 1997

1.997 Mikeys
#10. Application of a gut-immune co-culture system for the study of N-glycan-dependent host-pathogen interactions of Campylobacter jejuni
Cristina Y Zamora, Elizabeth M Ward, Jemila C Kester, Wen Li Kelly Chen, Jason G Velazquez, Linda G Griffith, Barbara Imperiali
An in vitro gut-immune co-culture model with apical and basal accessibility, designed to more closely resemble a human intestinal microenvironment, was employed to study the role of the Nlinked protein glycosylation (Pgl) pathway in Campylobacter jejuni pathogenicity. The gutimmune co-culture (GIC) was developed to model important aspects of the human small intestine by the inclusion of mucin producing goblet cells, human enterocytes, and dendritic cells, bringing together a mucus-containing epithelial monolayer with elements of the innate immune system. The utility of the system was demonstrated by characterizing host-pathogen interactions facilitated by N-linked glycosylation, such as host epithelial barrier functions, bacterial invasion and immunogenicity. Changes in human intestinal barrier functions in the presence of 11168 C. jejuni (wildtype) strains were quantified using GICs. The glycosylationdeficient strain 11168 ΔpglE was 100-fold less capable of adhering to and invading this intestinal model in cell infectivity...
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Authors: 7
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