Top 10 Biorxiv Papers Today in Microbiology


2.012 Mikeys
#1. A bacterial endosymbiont enables fungal immune evasion during fatal mucormycete infection
Herbert Itabangi, Poppy Sephton-Clark, Xin Zhou, Ignacio Insua, Mark Probert, Joao Correia, Patrick Moynihan, Teklegiorgis Gebremariam, Yiyou Gu, Lin Lin, Ashraf S Ibrahim, Gordon D Brown, Jason S King, Francisco Fernandez-Trillo, Elizabeth R Ballou, Kerstin Voelz
Environmentally ubiquitous fungal spores of the Mucorales order cause acute invasive infections through germination and evasion of the mammalian host immune system. Early phagocyte control of spore germination plays a key role in controlling infection, yet swelling Mucorales spores evade phagocytosis through an unknown mechanism. Here we investigate fungal immune evasion in a clinical isolate of Rhizopus microsporus and reveal the role of a bacterial endosymbiont, Ralsonia pickettii, in fungal pathogenesis. Analysis of phagocytosis rates in wild type and cured fungal isolates demonstrates a role for the endosymbiont in immune cell evasion through disruption of the cytoskeleton and phagosome maturation. Further analysis of bacterial secreted products revealed the presence of a previously uncharacterized secondary metabolite whose production is induced by the presence of the fungus. Analysis of the bacterial genome and condition-dependent RNAseq implicate a cryptic type I polyketide synthase. Subsequent analysis of wild type and...
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biorxivpreprint: A bacterial endosymbiont enables fungal immune evasion during fatal mucormycete infection https://t.co/h3Id7PCPIU #bioRxiv
biorxiv_micrbio: A bacterial endosymbiont enables fungal immune evasion during fatal mucormycete infection https://t.co/sYdQW1J57Y #biorxiv_micrbio
vivek_mutalik: RT @biorxiv_micrbio: A bacterial endosymbiont enables fungal immune evasion during fatal mucormycete infection https://t.co/sYdQW1J57Y #bi…
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Sample Sizes : [30, 15, 4, 5, 12, 5]
Authors: 16
Total Words: 18450
Unqiue Words: 6044

2.003 Mikeys
#2. Chimeric LuxR Transcription Factors Rewire Natural Product Regulation
Ruchira Mukherji, Somak Chowdhury, Pierre Stallforth
LuxR-type transcriptional activator proteins frequently flank bacterial biosynthetic gene clusters (BGCs) where they play a crucial role in regulating natural product formation. Only few bacterial BGCs are expressed under standard culturing conditions, thus modulation of flanking LuxRs is a powerful approach to activate silent clusters. Here, we show that exploiting the modular nature LuxR proteins and constructing chimeric LuxRs enables the activation of BGCs.
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vivek_mutalik: RT @biorxiv_micrbio: Chimeric LuxR Transcription Factors Rewire Natural Product Regulation https://t.co/szLqACRlUC #biorxiv_micrbio
soilmicrobe: RT @biorxiv_micrbio: Chimeric LuxR Transcription Factors Rewire Natural Product Regulation https://t.co/szLqACRlUC #biorxiv_micrbio
Mostlymicrobia: RT @biorxiv_micrbio: Chimeric LuxR Transcription Factors Rewire Natural Product Regulation https://t.co/szLqACRlUC #biorxiv_micrbio
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Sample Sizes : None.
Authors: 3
Total Words: 3162
Unqiue Words: 1329

2.0 Mikeys
#3. Mitigating Pandemic Risk with Influenza A Virus Field Surveillance at a Swine-Human Interface
Benjamin L Rambo-Martin, Matthew W Keller, Malania M Wilson, Jacqueline M Nolting, Tavis K Anderson, Amy L Vincent, Ujwal Bagal, Yunho Jang, Elizabeth B Neuhaus, C. Todd Davis, Andrew S Bowman, David E Wentworth, John R Barnes
Working overnight at a large swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, nanopore-sequenced 13 IAV genomes from samples collected, and in real-time, determined that these viruses posed a novel risk to humans due to genetic mismatches between the viruses and current pre-pandemic candidate vaccine viruses (CVV). We developed and used a portable IAV sequencing and analysis platform called Mia (Mobile Influenza Analysis) to complete and characterize full-length consensus genomes approximately 18 hours after unpacking the mobile lab. Swine are important animal IAV reservoirs that have given rise to pandemic viruses via zoonotic transmission. Genomic analyses of IAV in swine are critical to understanding pandemic risk of viruses in this reservoir, and characterization of viruses circulating in exhibition swine enables rapid comparison to current seasonal influenza vaccines and CVVs. The Mia system rapidly identified three genetically distinct swine IAV lineages from three subtypes: A(H1N1), A(H3N2) and...
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PromPreprint: Mitigating Pandemic Risk with Influenza A Virus Field Surveillance at a Swine-Human Interface https://t.co/jBGEBSf0EC
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Sample Sizes : [94]
Authors: 13
Total Words: 7775
Unqiue Words: 2571

1.998 Mikeys
#4. Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization
Bilal Alrubaye, Mussie Abraha, Ayidh Almansour, Mohit Bansal, Hong Wang, Young Min Kwon, Yan Huang, Billy Hargis, Xiaolun Sun
Despite reducing the prevalent foodborne pathogen Campylobacter jejuni in chickens decreases campylobacteriosis, few effective approaches are available. The aim of this study was to use microbial metabolic product bile acids to reduce C. jejuni chicken colonization. Broiler chicks were fed with deoxycholic acid (DCA), lithocholic acid (LCA), or ursodeoxycholic acid (UDCA). The birds were also transplanted with DCA modulated anaerobes (DCA-Anaero) or aerobes (DCA-Aero). The birds were infected with human clinical isolate C. jejuni 81-176 or chicken isolate C. jejuni AR101. Notably, C. jejuni 81-176 was readily colonized intestinal tract at d16 and reached an almost plateau at d21. Remarkably, DCA excluded C. jejuni cecal colonization at 100, 99.997, and 100% at 16, 21, and 28 days of age. Neither chicken ages of infection nor LCA or UDCA altered C. jejuni AR101 chicken colonization level, while DCA reduced 91% of the bacterium in chickens at d28. Notably, DCA diet reduced phylum Firmicutes but increased Bacteroidetes compared to...
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Authors: 9
Total Words: 8413
Unqiue Words: 2317

1.997 Mikeys
#5. Construction and validation of EGFP-expressing Staphylococcus aureus clinical strains for adhesion and internalization assays on epithelial cells
Sana Charaoui-Boukerzaza, Mohamed Fedy Morgene, Josselin Rigaill, Estelle Audoux, Zhiguo He, Florence Grattard, Anne Carricajo, Bruno Pozzetto, Philippe Berthelot, Elisabeth Botelho-Nevers, Paul O Verhoeven
Background: Staphylococcus aureus is both a major pathogen and a commensal bacterium in humans. It is able to adhere at the surface of epithelial cells of the anterior nares and can trigger its internalization inside these non-professional phagocytic cells. To better understand the interactions of clinical isolates with keratinocytes in the anterior nares, we developed and validated a one-step protocol expressing enhanced green fluorescent protein (EGFP) in S. aureus clinical strains with the aim to study adhesion to and internalization into mammalian cells. Methods: Twenty S. aureus clinical isolates belonging to clonal complexes 5, 8, 30, 45, 398 were selected for one-step transformation protocol with the EGFP-encoding plasmid pBSU101. EGFP expression was analysed by flow cytometry and confocal microscopy. Wild type and isogenic EGFP-expressing strains were compared for adhesion and internalization levels by using the HaCaT cell model. Results: Transformation was achieved in all the S. aureus strains regardless of their genetic...
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biorxivpreprint: Construction and validation of EGFP-expressing Staphylococcus aureus clinical strains for adhesion and internalization assays on epithelial cells https://t.co/gglu4dpCIA #bioRxiv
biorxiv_micrbio: Construction and validation of EGFP-expressing Staphylococcus aureus clinical strains for adhesion and internalization assays on ... https://t.co/d276gi22Wn #biorxiv_micrbio
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Sample Sizes : None.
Authors: 11
Total Words: 5558
Unqiue Words: 2159

1.997 Mikeys
#6. Effect of different forage-to-concentrate ratios on the structure of rumen bacteria and its relationship with nutrition levels and real-time methane production in sheep
Runhang Li, Zhanwei Teng, Chaoli Lang, Haizhu Zhou, Weiguang Zhong, Zhibin Ban, Xiaogang Yan, Huaming Yang, Mohammed Hamdy Farouk, Yujie Lou
Emission from ruminants has become the largest source of anthropogenic emission of methane in China. The structure of the rumen flora has a significant effect on methane production. To establish a more accurate prediction model for methane production, the rumen flora should be one of the most important parameters. The objective of the present study was to investigate the relationship among changes in rumen flora, nutrient levels, and methane production in sheep fed with the diets of different forage-to-concentration ratios, as well as to screen for significantly different dominant genera. Nine rumen-cannulated hybrid sheep were separated into three groups and fed three diets with forage-to-concentration ratios of 50:50, 70:30, and 90:10. Three proportions of the diets were fed according to a 3 × 3 incomplete Latin square, design during three periods of 15 d each. The ruminal fluid was collected for real-time qPCR, high-throughput sequencing and in vitro rumen fermentation in a new real-time fermentation system wit. Twenty-two...
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Sample Sizes : None.
Authors: 10
Total Words: 11153
Unqiue Words: 3948

1.996 Mikeys
#7. Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
Anna Cusco, Anna Salas, Celina Torre, Olga Francino
Long-read metagenomics -using single-molecule sequencers- has the potential to assembly entire genomes, even from complex metagenomics datasets. Using long-read metagenomics with Nanopore sequencing in pooled samples, we aim to improve the individual taxonomic profiles obtained with V4 16S rRNA massive sequencing and to assemble the fecal metagenome of healthy dogs. Fecal samples from healthy dogs were sequenced individually using V4 16S rRNA gene and in pools using a shallow metagenomics approach with Nanopore sequencing. Long-read metagenomics allowed us refining the V4 16S rRNA results up to the species level and determining the main bacterial species inhabiting on fecal microbiota of our cohort of healthy dogs. Among them, the most abundant were Fusobacterium varium; Megamonas hypermegale; Bacteroides vulgatus; Blautia hansenii; Clostridium perfringens; and Clostridoides difficile. Once performed the metagenome assembly, one contig was suggested to be circular and hit to an uncultured crAssphage. To conclude, shallow long-read...
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Authors: 4
Total Words: 0
Unqiue Words: 0

1.996 Mikeys
#8. Enhanced replication of mouse adenovirus type 1 following virus-induced degradation of protein kinase R (PKR)
Danielle E. Goodman, Carla D. Pretto-Kernahan, Tomas A. Krepostman, Kelly E. Carnahan, Katherine R. Spindler
Protein kinase R (PKR) plays a major role in activating host immunity during infection by sensing dsRNA produced by viruses. Once activated by dsRNA, PKR phosphorylates the translation factor eIF2α, halting cellular translation. Many viruses have methods of inhibiting PKR activation or its downstream effects, circumventing protein synthesis shutdown. These include sequestering dsRNA or producing proteins that bind to and inhibit PKR activation. Here we describe our finding that in multiple cell types, PKR was depleted during mouse adenovirus type 1 (MAV-1) infection. MAV-1 did not appear to be targeting PKR at a transcriptional or translational level because total PKR mRNA levels and levels of PKR mRNA bound to polysomes were unchanged or increased during MAV-1 infection. However, inhibiting the proteasome reduced the PKR depletion seen in MAV-1-infected cells, whereas inhibiting the lysosome had no effect. This suggests that proteasomal degradation alone is responsible for PKR degradation during MAV-1 infection. Time course...
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Authors: 5
Total Words: 18353
Unqiue Words: 4545

1.996 Mikeys
#9. Assays for monitoring Toxoplasma gondii infectivity in the laboratory mouse
Qiuling Wang, L. David Sibley
Toxoplasma is a widespread parasite of animals including many rodents that are a natural part of the transmission cycle between cats, which serve as the definitive host. Although wild rodents, including house mice, are relatively resistant, laboratory mice are highly susceptible to infection. As such, laboratory mice and have been used to compare pathogenesis of natural variants, and to evaluate the contributions of both host and parasite genes to infection. Protocols are provided here for evaluating acute and chronic infection with different parasite strains in laboratory mice. These protocols should provide uniform standards for evaluating natural variants and attenuated mutants and for comparing outcomes across different studies and between different laboratories.
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Sample Sizes : None.
Authors: 2
Total Words: 9399
Unqiue Words: 3476

1.996 Mikeys
#10. Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients
Anuradha Ravi, Fenella Halstead, Amy Bamford, Anna Casey, Nicholas Thomson, Willem van Schaik, Catherine Snelson, Robert Goulden, Ebenezer Foster-Nyarko, George Savva, Tony Whitehouse, Mark PALLEN, Beryl Oppenheim
Background: For long-stay patients on the adult intensive care unit, the gut microbiota plays a key role in determining the balance between health and disease. However, it remains unclear which ICU patients might benefit from interventions targeting the gut microbiota or the pathogens therein. Methods: We undertook a prospective observational study of twenty-four ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Results: Two-thirds of patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in ICU, often accompanied by absence or loss of beneficial commensal bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but administration of other antibiotics, including piperacillin-tazobactam, failed to trigger statistically detectable changes in microbial diversity....
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Sample Sizes : [228]
Authors: 13
Total Words: 10452
Unqiue Words: 4067

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