Top 10 Biorxiv Papers Today in Microbiology


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#1. Glutamate dehydrogenase (Gdh2)-dependent alkalization is dispensable for escape from macrophages and virulence of Candida albicans
Fitz G.S. Silao, Kicki Ryman, Tong Jiang, Meliza Ward, Nicolas Hansmann, Ning-Ning Liu, Changbin Chen, Per O. Ljungdahl
Candida albicans cells depend on the energy derived from amino acid catabolism to induce and sustain hyphal growth inside phagosomes of engulfing macrophages. The concomitant deamination of amino acids is thought to neutralize the acidic microenvironment of phagosomes, a presumed requisite for survival and initiation of hyphal growth. Here, in contrast to an existing model, we show that mitochondrial-localized NAD+-dependent glutamate dehydrogenase (GDH2) catalyzing the deamination of glutamate to α-ketoglutarate, and not the cytosolic urea amidolyase (DUR1,2), accounts for the observed alkalization of media when amino acids are the sole sources of carbon and nitrogen. C. albicans strains lacking GDH2 (gdh2-/-) are viable and do not extrude ammonia on amino acid-based media. Environmental alkalization does not occur under conditions of high glucose (2%), a finding attributable to glucose-repression of GDH2expression and mitochondrial function. Consistently, inhibition of oxidative phosphorylation or mitochondrial translation by...
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Authors: 8
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#2. A partial pathogenicity chromosome in Fusarium oxysporum is sufficient to cause disease and can be horizontally transferred
Jiming Li, Like Fokkens, Lee James Conneely, Martijn Rep
During host colonization, plant pathogenic fungi secrete proteins, called effectors, to facilitate infection. Collectively, effectors may defeat the plant immune system, but usually not all effectors are equally important for infecting a particular host plant. In Fusarium oxysporum f.sp. lycopersici, all known effector genes – also called SIX genes – are located on a single accessory chromosome which is required for pathogenicity and can also be horizontally transferred to another strain. To narrow down the minimal region required for virulence, we selected partial pathogenicity chromosome deletion strains by fluorescence-assisted cell sorting of a strain in which the two arms of the pathogenicity chromosome were labelled with GFP and RFP, respectively. By testing the virulence of these deletion mutants, we show that the complete long arm and part of the short arm of the pathogenicity chromosome are not required for virulence. In addition, we demonstrate that smaller versions of the pathogenicity chromosome can also be transferred...
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biorxivpreprint: A partial pathogenicity chromosome in Fusarium oxysporum is sufficient to cause disease and can be horizontally transferred https://t.co/1GuMIRGEkz #bioRxiv
biorxiv_micrbio: A partial pathogenicity chromosome in Fusarium oxysporum is sufficient to cause disease and can be horizontally transferred https://t.co/NQDh13Zwxv #biorxiv_micrbio
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Authors: 4
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#3. A single nonsynonymous mutation on gene encoding E protein of Zika virus leads to increased neurovirulence in vivo
Zhihua Liu, Yawei Zhang, Mengli Cheng, Ningning Ge, Jiayi Shu, Zhiheng Xu, Yigang Tong, Chengfeng Qin, Xia Jin
Zika virus can infect a wide range of tissues including the developmental brain of human fetuses, causing from mild to severe clinical diseases. Whether its genetic characteristics impacts on viral pathogenesis is incompletely understood. We have obtained viral variants through serially passage of a clinical Zika virus isolate (SW01) in neonatal mice in vivo and found some of which exhibited markedly increased virulence and neurotropism. By deep sequencing analysis, the more pathogenic viral variants were found to contain four dominant nonsynonymous nucleotide mutations on genes encoding E and NS2A proteins. Further investigation using molecularly cloned viruses revealed that a single 67D (Aspatic acid) to N (Asparagine) substitution on E protein is sufficient to confer the increased virulence and neurotropism. These findings provide new insight into Zika virus pathogenesis and suggest novel targets for the development of therapeutics.
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biorxivpreprint: A single nonsynonymous mutation on gene encoding E protein of Zika virus leads to increased neurovirulence in vivo https://t.co/ogbtcroMaj #bioRxiv
biorxiv_micrbio: A single nonsynonymous mutation on gene encoding E protein of Zika virus leads to increased neurovirulence in vivo https://t.co/EBQLyXxjxW #biorxiv_micrbio
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Authors: 9
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#4. Ethanol tolerance in Escherichia coli DH5-Alpha developed by serial exposure to sublethal doses is conferred to wild strains by horizontal gene transfer
Ronak Borana, Shreya Bari
Microorganisms evolve novel mechanisms and pathways to mitigate various stresses. These are developed by the accumulation of beneficial mutations over many generations. Such adaptations are often transferred from mutant microorganisms that develop it intrinsically to wild ones through horizontal gene transfer (HGT). It allows the latter to acquire favourable traits without having to employ resources to natively evolve. We ascertained this in Escherichia coli by first developing tolerance to ethanol, a potent disinfectant, by laboratory evolution and then transmitting it to the wild strain by HGT. Naturally, wild type E. coli cannot survive beyond 35% v/v ethanol in LB media. By serially increasing the concentration of ethanol by 5% v/v and selecting the surviving colonies, we were able to impose an artificial selection pressure. This in vitro microevolution increased the ethanol tolerance in our mutant to 75% v/v. To test if this tolerance could be transferred to the wild strain through HGT, we meticulously exposed the ancestral...
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#5. Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste
Jacob Bruun Joergensen, Amaru M. Djurhuus, Alexander Byth Carstens, Witold Piotr Kot, Cindy E. Morris, Lars Hestbjerg Hansen
Three phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.
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biorxivpreprint: Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste https://t.co/4qsKbmxz75 #bioRxiv
biorxiv_micrbio: Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste https://t.co/Rfvb8kkO6o #biorxiv_micrbio
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Authors: 6
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#6. Evolution, geographic spreading, and demographic distribution of Enterovirus D68
Emma B Hodcroft, Robert Dyrdak, Cristina Andres, Adrian Egli, Josiane Reist, Diego Garcia Martinez de Artola, Julia Alcoba Florez, Hubert G. M. Niesters, Andres Anton, Randy Poelman, Marijke Reynders, Elke Wollants, Richard A. Neher, Jan Albert
Background: Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. Methods: We collected samples from several European countries during the 2018 outbreak and determined 53 near full-length genome ('whole genome') sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences. Findings: In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68...
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biorxivpreprint: Evolution, geographic spreading, and demographic distribution of Enterovirus D68 https://t.co/9gSdmtFbew #bioRxiv
biorxiv_micrbio: Evolution, geographic spreading, and demographic distribution of Enterovirus D68 https://t.co/nG3oKUqki5 #biorxiv_micrbio
firefoxx66: #EVD68 may have *significant undetected circulation in adults* – evidence in our latest paper suggests. “Evolution, geographic spreading, & demographic distribution of #Enterovirus #D68” PrePrint out now – please go read! https://t.co/uBhAhWlwty Summary thread below… (1/15)
DSL79566674: RT @biorxivpreprint: Evolution, geographic spreading, and demographic distribution of Enterovirus D68 https://t.co/9gSdmtFbew #bioRxiv
Diard_Lab: RT @biorxivpreprint: Evolution, geographic spreading, and demographic distribution of Enterovirus D68 https://t.co/9gSdmtFbew #bioRxiv
jseden1: RT @biorxivpreprint: Evolution, geographic spreading, and demographic distribution of Enterovirus D68 https://t.co/9gSdmtFbew #bioRxiv
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#7. Competitive exclusion of uropathogenic E. coli biofilm by Salmonella through matrix inhibition
Sandeep Miryala, Chandramohan S, Srinandan Chakravarthy
Biofilm is a predominant lifestyle of bacteria in host and non-host environments with cell collectives and extracellular matrix as the defining principles of biofilm. Several factors trigger biofilm formation including response to competition. Urinary tract infections (UTI) are highly prevalent worldwide mainly caused by uropathogenic E. coli (UPEC), which progresses into chronic form due to the biofilm formation by the pathogen. In this study, we hypothesized that competition for territorial space could occur between species by intervening in the biofilm matrix production, particularly of UPEC, thereby reducing its colonizing ability. UPEC colony displays different morphology in congo red media based on matrix production, which we exploited for screening bacterial isolates capable of inhibiting the matrix. This was validated by using the cell-free supernatants of the isolates to impair UPEC biofilm. Isolates that inhibited matrix production belonged to species of Shigella , Escherichia , Enterobacter , and Salmonella from...
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Sample Sizes : [4]
Authors: 3
Total Words: 8041
Unqiue Words: 2646

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#8. A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels
Zhang Wang, Haiyue Liu, Fengyan Wang, Yuqiong Yang, Xiaojuan Wang, Boxuan Chen, Martin Stampfli, Hongwei Zhou, Wensheng Shu, Christopher Brightling, Zhenyu Liang, Rongchang Chen
Little is known about the species and strain-level diversity of the airway microbiome, and its implication in chronic obstructive pulmonary disease (COPD). Here we report the first comprehensive analysis of the COPD airway microbiome at species and strain-levels. The full-length 16S rRNA gene was sequenced from sputum in 98 stable COPD patients and 27 age-matched healthy controls, using the third-generation Pacific Biosciences sequencing platform. Individual species within the same genus exhibited reciprocal relationships with COPD and disease severity. Species dominant in health can be taken over by another species within the same genus in GOLD IV patients. Such turnover was also related to enhanced symptoms and exacerbation frequency. Ralstonia mannitolilytica, an opportunistic pathogen, was significantly increased in COPD frequent exacerbators. There were inflammatory phenotype-specific associations of microbiome at the species-level. One group of four pathogens including Haemophilus influenzae and Moraxella catarrhalis, were...
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biorxivpreprint: A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels https://t.co/d2XFXGA5QI #bioRxiv
biorxiv_micrbio: A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels https://t.co/8YShnfMYL4 #biorxiv_micrbio
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Sample Sizes : [27, 98]
Authors: 12
Total Words: 8585
Unqiue Words: 3233

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#9. Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species
Nikoline S Olsen, Witold Kot, Laura M. F. Junco, Lars H Hansen
Phages drive bacterial diversity - profoundly influencing diverse microbial communities, from microbiomes to the drivers of global biogeochemical cycling. The vast genomic diversity of phages is gradually being uncovered as >8000 phage genomes have now been sequenced. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples (0.5 ml) and identified 136 phages of which 104 are unique phage species and 91 represent novel species, including several novel lineages. These phages are estimated to represent roughly a third of the true diversity of Escherichia phages in Danish wastewater. The novel phages are remarkably diverse and represent four different families Myoviridae, Siphoviridae, Podoviridae and Microviridae. They group into 14 distinct clusters and nine singletons without any substantial similarity to other phages in the dataset. Their genomes vary drastically in length from merely 5 342 bp to 170 817 kb, with an impressive span of GC contents ranging from 35.3% to...
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biorxivpreprint: Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species https://t.co/zO04ZPt56A #bioRxiv
biorxiv_micrbio: Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species https://t.co/wbfsg29YRj #biorxiv_micrbio
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Authors: 4
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#10. The Requirement For US28 During Cytomegalovirus Latency Is Independent Of US27 And US29 Gene Expression
Benjamin A. Krishna, Amanda B. Wass, Rajashri Sridharan, Christine M. O'Connor
The ability to establish a latent infection with periodic reactivation events ensures herpesviruses, like human cytomegalovirus (HCMV), lifelong infection and serial passage. The host-pathogen relationship throughout HCMV latency is complex, though both cellular and viral factors influence the equilibrium between latent and lytic infection. We and others have shown one of the viral-encoded G protein-coupled receptors, US28, is required for HCMV latency. US28 potentiates signals both constitutively and in response to ligand binding, and we previously showed deletion of the ligand binding domain or mutation of the G protein-coupling domain results in the failure to maintain latency similar to deletion of the entire US28 open reading frame (ORF). Interestingly, a recent publication detailed an altered phenotype from that previously reported, showing US28 is required for viral reactivation rather than latency, suggesting the US28 ORF deletion impacts transcription of the surrounding genes. Here, we show an independently generated...
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biorxivpreprint: The Requirement For US28 During Cytomegalovirus Latency Is Independent Of US27 And US29 Gene Expression https://t.co/FVNzlSNp69 #bioRxiv
biorxiv_micrbio: The Requirement For US28 During Cytomegalovirus Latency Is Independent Of US27 And US29 Gene Expression https://t.co/YL6HXB1rW1 #biorxiv_micrbio
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Authors: 4
Total Words: 0
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