Top 10 Biorxiv Papers Today in Microbiology


2.041 Mikeys
#1. The microbiome wants what it wants: microbial evolution overtakes experimental host-mediated indirect selection
Jigyasa Arora, Margaret Mars Brisbin, Alexander Mikheyev
Microbes ubiquitously inhabit animals and plants, often affecting their host's phenotype. As a result, even in a constant genetic background, the host's phenotype may evolve through indirect selection on the microbiome. 'Microbiome engineering' offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four rounds of selection. In each round, we used sterile eggs from the same inbred population, and assayed fly mean eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but selection had no effect. 16S sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in alpha diversity...
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biorxivpreprint: The microbiome wants what it wants: microbial evolution overtakes experimental host-mediated indirect selection https://t.co/h4SLbxWrNJ #bioRxiv
biorxiv_micrbio: The microbiome wants what it wants: microbial evolution overtakes experimental host-mediated indirect selection https://t.co/tFqTmoz4OY #biorxiv_micrbio
MargaretBrisbin: A large amount of my 1st 1.5 years at oist were spent taking care of flies, making food, cleaning vials, counting, sorting, transferring- and finally ... here are some results: https://t.co/KZqLVM2pVM - #microbiome #drosophila #fruitflies #microbes
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Authors: 3
Total Words: 6415
Unqiue Words: 2123

2.028 Mikeys
#2. Assaying Chlamydia pneumoniae persistence in monocyte-derived macrophages identifies schisandrin lignans as phenotypic switchers
Eveliina Taavitsainen, Maarit Kortesoja, Leena Hanski
Antibiotic-tolerant persister bacteria involve frequent treatment failures, relapsing infections and the need for extended antibiotic treatment. Taking persisters into account in susceptibility assays is thus an essential success factor in antibacterial drug discovery. The virulence of the obligate intracellular bacterium Chlamydia pneumoniaeis tightly linked to its propensity for persistence, but current susceptibility screening on this gram-negative respiratory pathogen relies on permissive epithelial cells. To establish an improved antichlamydial susceptibility assay allowing the analysis of both actively growing and persister bacteria, we studied C. pneumoniae clinical isolate CV-6 infection kinetics in THP-1 macrophages by qPCR and quantitative culture. Indicated by the steady increase of chlamydial genome copy numbers and infectious progeny as well as the failure of azithromycin to eradicate the intracellular forms of the bacterium, the macrophages were found to harbor a subpopulation of persister C. pneumoniaecells. The...
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biorxivpreprint: Assaying Chlamydia pneumoniae persistence in monocyte-derived macrophages identifies schisandrin lignans as phenotypic switchers https://t.co/8JIZE7impD #bioRxiv
biorxiv_micrbio: Assaying Chlamydia pneumoniae persistence in monocyte-derived macrophages identifies schisandrin lignans as phenotypic switchers https://t.co/LMjYGfUdc8 #biorxiv_micrbio
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Authors: 3
Total Words: 8297
Unqiue Words: 2838

2.026 Mikeys
#3. Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn
Magdalena J Mayr, Matthias Zimmermann, Jason Dey, Andreas Brand, Helmut Buergmann
Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lacustrine sediments produce large amounts of methane, which accumulate in oxygen-depleted hypolimnia of stratified lakes. Due to climate change and progressing eutrophication, the number of lakes with hypolimnetic methane storage may increase in the future. However, whether stored methane eventually reaches the atmosphere during lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. We show that the methanotroph assemblage in a mixing lake undergoes a substantial bloom and ecological succession. As a result, the methane oxidation capacity of the mixed layer kept pace with the methane supplied from the hypolimnion and most of the stored methane was oxidized. Our work demonstrates a previously unknown component of freshwater methanotroph ecology illuminating the mechanisms limiting methane transfer from lakes to the atmosphere.
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biorxivpreprint: Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn https://t.co/IKMPiWAWAW #bioRxiv
biorxiv_micrbio: Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn https://t.co/p2khfHYHlL #biorxiv_micrbio
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Authors: 5
Total Words: 0
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2.026 Mikeys
#4. Designed Nanoparticles Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes
Dustin M McCraw, Mallory L Myers, Neetu M Gulati, John R Gallagher, Alexander J Kim, Udana Torian, Audray K Harris
Despite the availability of seasonal vaccines and antiviral medications, influenza virus continues to be a major health concern and pandemic threat due to the continually changing antigenic regions of the major surface glycoprotein, hemagglutinin (HA). One emerging strategy for the development of more efficacious seasonal and universal influenza vaccines is structure-guided design of nanoparticles that display conserved regions of HA, such as the stem. Using the H1 HA subtype to establish proof of concept, we found that an alpha-helical fragment (helix-A) from the conserved stem region can be displayed on nanoparticles. The stem region of HA on these nanoparticles is immunogenic and the nanoparticles are biochemically robust in that heat exposure did not destroy the particles and immunogenicity was retained. Furthermore, H1-nanoparticles protected mice from lethal challenge with H1N1 influenza virus. Importantly, antibodies elicited by these nanoparticles demonstrated homosubtypic and heterosubtypic cross-reactivity. The helix-A...
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biorxivpreprint: Designed Nanoparticles Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes https://t.co/LXqhvGyqE6 #bioRxiv
biorxiv_micrbio: Designed Nanoparticles Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes https://t.co/eEB5VBIW87 #biorxiv_micrbio
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Authors: 7
Total Words: 0
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2.026 Mikeys
#5. Cryptic prophage-encoded small protein DicB protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins
Preethi T. Ragunathan, Carin K Vanderpool
Bacterial genomes harbor cryptic prophages that have lost genes required for induction, excision from host chromosomes, or production of phage progeny. Escherichia coli K12 strains contain a cryptic prophage Qin that encodes a small RNA, DicF, and small protein, DicB, that have been implicated in control of bacterial metabolism and cell division. Since DicB and DicF are encoded in the Qin immunity region, we tested whether these gene products could protect the E. coli host from bacteriophage infection. Transient expression of the dicBF operon yielded cells that were ~100-fold more resistant to infection by λ phage than control cells, and the phenotype was DicB-dependent. DicB specifically inhibited infection by λ and other phages that use ManYZ membrane proteins for cytoplasmic entry of phage DNA. In addition to blocking ManYZ-dependent phage infection, DicB also inhibited the canonical sugar transport activity of ManYZ. Previous studies demonstrated that DicB interacts with MinC, an FtsZ polymerization inhibitor, causing MinC...
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biorxivpreprint: Cryptic prophage-encoded small protein DicB protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins https://t.co/3Y0Q90ZrUw #bioRxiv
biorxiv_micrbio: Cryptic prophage-encoded small protein DicB protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins https://t.co/LyXT8Dqxem #biorxiv_micrbio
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Authors: 2
Total Words: 13891
Unqiue Words: 3670

2.014 Mikeys
#6. Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure.
Petros C. Karakousis, William M Matern, Joel Bader, Robert L Jenquin
Mycobacterium avium (Mav) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying structural lung disease. Generally, Mav infection is treated with 2-3 antimicrobial drugs for at least 12 months. Identification of genes essential for Mav growth may yield novel strategies for improving curative therapy. We have generated saturating genome-wide transposon mutant pools in a commonly used laboratory strain of Mycobacterium avium subsp. hominissuis (MAC109) and developed a computational technique for classifying annotated genomic features as essential (ES), growth defect (GD), growth advantage (GA), or no-effect (NE) based on the in vitro effect of disruption by transposon. We identified 270 features as ES with 230 of these overlapping with ES features in Mycobacterium tuberculosis. These results may be useful for identifying drug targets or for informing studies requiring genetic manipulation of Mycobacterium avium, which should seek to avoid...
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Reproduces our results presented in our upcoming paper: "Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure."

Repository: essential_genes
User: joelbader
Language: Python
Stargazers: 0
Subscribers: 1
Forks: 0
Open Issues: 0
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Authors: 4
Total Words: 7136
Unqiue Words: 2495

2.01 Mikeys
#7. Identification and evolution of avian endogenous foamy viruses
Yicong Chen, Xiaoman Wei, Guojie Zhang, Edward Holmes, Jie Cui
A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time-periods. Endogenous foamy viruses (EFVs) are rare, and to date have only been found in a limited number of genomes from mammals, amphibians, reptiles and fish. By screening 510 avian genomes we identified endogenous foamy viruses in avian species - from the Maguari Stork (Ciconia maguari) and Oriental Stork (C. boyciana). Phylogenetic analysis and analysis of the genome structures and flanking sequences indicated a single origin of EFVs into Ciconia during evolutionary history, and the marked incongruence with the host phylogeny suggested that this integration event occurred independently in birds. In sum, this study provides evidence that birds can be infected with foamy viruses, filling the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
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biorxivpreprint: Identification and evolution of avian endogenous foamy viruses https://t.co/sbTNwOTjgw #bioRxiv
biorxiv_micrbio: Identification and evolution of avian endogenous foamy viruses https://t.co/ZDxksX1qJr #biorxiv_micrbio
Inannamarduk: RT @biorxivpreprint: Identification and evolution of avian endogenous foamy viruses https://t.co/sbTNwOTjgw #bioRxiv
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2.009 Mikeys
#8. Activation of the Extracytoplasmic Function σ factor σP by β-lactams in Bacillus thuringiensis requires the site-2 protease RasP
Theresa D Ho, Kelsie M. Nauta, Ute Muh, Craig D. Ellermeier
Bacteria can utilize alternative σ factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative σ factors are the Extracytoplasmic Function (ECF) σ factors. σP is an ECF σ factor found in Bacillus anthracis , B. cereus , and B. thuringiensis . Previous work showed σP is induced by ampicillin, a β-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of σP is controlled or what other antibiotics may activate σP. Here we report that activation of σP is specific to a subset of β-lactams and σP is required for resistance to these β-lactams. We demonstrate that activation of σP is controlled by the proteolytic destruction of the anti-σ factor, RsiP, and that degradation of RsiP requires multiple proteases. Upon exposure to β-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N-terminus of RsiP is further degraded...
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biorxivpreprint: Activation of the Extracytoplasmic Function σ factor σP by β-lactams in Bacillus thuringiensis requires the site-2 protease RasP https://t.co/z06AqUwPac #bioRxiv
biorxiv_micrbio: Activation of the Extracytoplasmic Function σ factor σP by β-lactams in Bacillus thuringiensis requires the site-2 protease RasP https://t.co/n8DGSODHyd #biorxiv_micrbio
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Authors: 4
Total Words: 11740
Unqiue Words: 3552

2.009 Mikeys
#9. A porcine ex vivo lung perfusion model to investigate bacterial pathogenesis
Amy Dumigan, Marianne Fitzgerald, Joana Sa-Pessoa, Umar Hamid, Cecilia O'kane, Danny F McAuley, Jose A Bengoechea
The use of animal infection models is essential to understand microbial pathogenesis and to develop and test treatments. Insects, and 2D and 3D tissue models are increasingly being used as surrogate for mammalian models. However, there are concerns whether these models recapitulate the complexity of host-pathogen interactions. Here, we developed the ex vivo lung perfusion (EVLP) model of infection using porcine lungs to investigate Klebsiella pneumoniae -triggered pneumonia as model of respiratory infections. The porcine EVLP model recapitulates features of K. pneumoniae -induced pneumonia lung injury. This model is also useful to assess the pathogenic potential of K. pneumoniae as we observed that the attenuated Klebsiella capsule mutant strain caused less pathological tissue damage with a concomitant decrease in the bacterial burden compare to lungs infected with the wild type. The porcine EVLP model allows assessment of inflammatory responses following infection; similar to the mouse pneumonia model, we observed an increase of...
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staphTCD: RT @biorxiv_micrbio: A porcine ex vivo lung perfusion model to investigate bacterial pathogenesis https://t.co/F2feXqSORq #biorxiv_micrbio
mcclean_siobhan: RT @biorxiv_micrbio: A porcine ex vivo lung perfusion model to investigate bacterial pathogenesis https://t.co/F2feXqSORq #biorxiv_micrbio
MonaSusanJohan1: RT @biorxivpreprint: A porcine ex vivo lung perfusion model to investigate bacterial pathogenesis https://t.co/mVxeJ7K5Hr #bioRxiv
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2.009 Mikeys
#10. Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity.
Jose Francisco Cobo-Diaz, Fabienne Legrand, Gaetan Le Floch, Adeline Picot
Fusarium graminearum ( Fg ) can cause different diseases in cereals and maize crops worldwide, and a correct management of previous crop residues could decrease disease incidence and/or severity. Bacterial, fungal and Fusarium communities were studied by metabarcoding approach in 8 agricultural fields with wheat-maize rotation system in Brittany, France, during three years. Additionally, shift in microbial communities were evaluated under mesocosm experiments in soils amended or not with maize residues and/or Fg isolate. Bacterial communities composition were highly influenced by crop soil origin in both environmental and mesocosm soils, while bacteria co-occurrence network complexity was decreased by maize residues in environmental samples and Fg treatment in mesocosm samples. Maize residues altered slightly bacteria-fungi co-occurrence networks, while all treatments on mesoscosm experiments showed lower complexity in bacteria-fungi networks than Control Soil treatment. A clear input of fungal genera Epicoccum , Fusarium ,...
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biorxivpreprint: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity. https://t.co/yPjKTwFqOP #bioRxiv
biorxiv_micrbio: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity. https://t.co/9aNJSaGPqP #biorxiv_micrbio
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Authors: 4
Total Words: 13971
Unqiue Words: 4171

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