Top 10 Biorxiv Papers Today in Microbiology


2.051 Mikeys
#1. Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection
Amin Addetia, Lauren C Tantalo, Michelle J Lin, Hong Xie, Meei-Li Huang, Christina Marra, Alexander L. Greninger
Developing a vaccine against Treponema pallidum subspecies pallidum, the causative agent of syphilis, remains a public health priority. Syphilis vaccine design efforts have been complicated by lack of an in vitro T. pallidum culture system, prolific antigenic variation in outer membrane protein TprK, and lack of functional annotation for nearly half of the genes. Understanding the genetic basis of T. pallidum reinfection can provide insights into variation among strains that escape cross-protective immunity. Here, we present comparative genomic sequencing and deep, full-length tprK profiling of two T. pallidum isolates from blood from the same patient that were collected six years apart. Notably, this patient was diagnosed with syphilis four times, with two of these episodes meeting the definition of neurosyphilis, during this interval. Outside of the highly variabletprK gene, we identified 14 coding changes in 13 genes. Nine of these genes putatively localized to the periplasmic or outer membrane spaces, consistent with a...
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biorxivpreprint: Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection https://t.co/RZgZmN3dwL #bioRxiv
biorxiv_micrbio: Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection https://t.co/zH44z5lcWV #biorxiv_micrbio
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Repository: tprk
User: greninger-lab
Language: R
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Authors: 7
Total Words: 10111
Unqiue Words: 3311

2.017 Mikeys
#2. Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy
Andrew Oliver, Brandon LaMere, Claudia Weihe, Stephen Wandro, Karen Lindsay, Pathik Wadhwa, David Mills, David T Pride, Oliver Fiehn, Trent Northen, Markus de Raad, Huiying Li, Jennifer B.H. Martiny, Susan Lynch, Katrine Whiteson
Background: Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well adapted microbes, which are able to survive in a narrow pH range. In comparison to other human-associated microbes, vaginal microbes are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. Methods: Using 16S rRNA and ITS amplicon sequencing, we characterized the cervicovaginal microbiomes of 18 healthy women throughout the three trimesters of pregnancy. Shotgun metagenomic sequencing permitted refinement of the taxonomy established by amplicon sequencing, and identification of functional genes. Additionally, we analyzed saliva and urine metabolomes using GC-TOF and LC-MS/MS lipidomics approaches for samples from mothers and their infants through the first year of life. Results: Amplicon sequencing revealed most women had either a simple...
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biorxivpreprint: Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy https://t.co/PdwAUfrS01 #bioRxiv
biorxiv_micrbio: Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy https://t.co/utWZqcPxwi #biorxiv_micrbio
CTMRBio: RT @biorxiv_micrbio: Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy https://t.co/utWZqcPxwi #biorxiv…
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Authors: 15
Total Words: 0
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2.003 Mikeys
#3. Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice.
Maria G Noval, Margarita V Rangel, Katherine E Johnson, Elfie De Jesus, Adam Gerber, Samantha Schuster, Ken Cadwell, Elodie Ghedin, Kenneth A Stapleford
The fundamental basis of how arboviruses evolve in nature and what regulates the adaptive process remain unclear. To address this problem, we established a Zika virus (ZIKV) vector-borne transmission system in immunocompromised mice that mimics evolutionary characteristics of ZIKV infection in humans. Using this system, we defined factors that influence the evolutionary landscape of ZIKV infection and show that transmission route and specific organ microenvironments impact viral diversity and defective viral genome (DVG) production. In addition, we identified in mice the emergence of ZIKV mutants previously seen in natural infections, including variants present in currently circulating strains, as well as mutations unique to the mouse infections. With these studies, we have established an insect-to-mouse transmission model to study ZIKV evolution. We also defined how organ microenvironments and infection route impact the ZIKV evolutionary landscape, providing a deeper understanding of the factors that regulate arbovirus evolution...
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Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice.

Repository: ZIKV_Analysis
User: GhedinLab
Language: Python
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Sample Sizes : [3, 7]
Authors: 9
Total Words: 16143
Unqiue Words: 4378

2.003 Mikeys
#4. Production of Insoluble Starch-Like Granules in Escherichia coli by Modification of the Glycogen Synthesis Pathway
Joseph John White, Natasha Cain, Chris French
While investigating the conversion of cellulosic biomass to starch-like materials for industrial use, it was observed that the overexpression of native ADP-glucose pyrophosphorylase GlgC in Escherichia coli led to the formation of insoluble polysaccharide granules within the cytoplasm, occupying a large fraction of the cell volume, as well as causing an overall increase in cellular polysaccharide content. TEM microscopy revealed that the granules did not have the lamellar structure of starch, but rather an irregular, clustered structure. On starvation, cells overexpressing GlgC appeared unable to fully degrade their polysaccharide material and granules were still clearly visible in cultures after 8 days of starvation. Interestingly, the additional overexpression of the branching enzyme GlgB eliminated the production of granules and led to a further increase in cellular polysaccharides. GlgC is generally thought to be responsible for the rate-limiting step of glycogen synthesis. Our interpretation of these results is that excess...
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mabohash: Production of Insoluble Starch-Like Granules in Escherichia coli by Modification of the Glycogen Synthesis Pathway by White et al. 2019. https://t.co/UeqeRrYdWG
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Authors: 3
Total Words: 9082
Unqiue Words: 2714

1.998 Mikeys
#5. An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery
Garrett C McCarthy, Sydney Christian Morgan, Jonathan T Martiniuk, Brianne L Newman, Vivien Measday, Daniel M Durall
Saccharomyces cerevisiae is the primary yeast species responsible for most fermentations in winemaking. However, other yeasts, including Saccharomyces uvarum, have occasionally been found conducting commercial fermentations around the world. S. uvarum is typically associated with white wine fermentations in cool-climate wine regions, and has been identified as the dominant yeast in fermentations from France, Hungary, northern Italy, and, recently, Canada. However, little is known about how the origin and genetic diversity of the Canadian S. uvarum population relates to strains from other parts of the world. In this study, a highly diverse S. uvarum population was found dominating uninoculated commercial fermentations of Chardonnay grapes sourced from two different vineyards. Most of the strains identified were found to be genetically distinct from S. uvarum strains isolated around the world. Of the 106 strains of S. uvarum identified in this study, four played a dominant role in the fermentations, with some strains predominating...
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biorxivpreprint: An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery https://t.co/GWo1muA0KT #bioRxiv
biorxiv_micrbio: An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a ... https://t.co/jQSyJ3qjJd #biorxiv_micrbio
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Authors: 6
Total Words: 15843
Unqiue Words: 4698

1.997 Mikeys
#6. Vibrio deploys Type 2 secreted lipase to esterify cholesterol with host fatty acids and mediate cell egress
Marcela de Souza Santos, Suneeta Chimalapati, Ann Ray, Wan-Ru Lee, Giomar Rivera-Cancel, Alex Lafrance, Gonçalo Vale, Matt Mitsche, Jeffrey G McDonald, Jen Liou, Kim Orth
Pathogens find diverse niches for survival inside host cells where replication occurs in a relatively protected environment. Vibrio parahaemolyticus, a facultative intracellular pathogen, uses its type 3 secretion system 2 (T3SS2) to invade and replicate inside host cells. However, after extensive analysis, the T3SS2 pathogenicity island appeared to lack a mechanism for egress of this bacterium from the invaded host cell. Using a combination of cell biology, microbial genetics and lipid biochemistry, we found that VPA0226, a constitutively secreted lipase, is required for escape of Vibrio parahaemolyticus from host cells. Remarkably, this lipase must be delivered into the host cytoplasm where it preferentially uses fatty acids associated with innate immune response (i.e. arachidonic acid, 20:4) to esterify cholesterol, weakening the plasma membrane and allowing egress of the bacteria. This study reveals the resourcefulness of microbes and the interplay between virulence systems to evolve an ingenious scheme for survival and escape.
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Authors: 11
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1.997 Mikeys
#7. The urinary tract microbiome in older women exhibits host genetics and environmental influences
Adewale S Adebayo, Gail Ackermann, Ruth C. E. Bowyer, Philippa M Wells, Gregory Humphrey, Rob Knight, Tim D Spector, Claire J Steves
The urinary microbiome is a relatively unexplored niche despite the fact that we now know that it is not sterile. Moreover urinary microbes, especially in ageing populations, are associated with morbidity even when infection is subsequently not proven. We present the first large-scale study to explore factors defining urinary microbiome composition in community-dwelling older adult women without clinically active infection. Using 1600 twins, we estimate the contribution of genetic and environmental factors to variation in microbiome using both 16S and shotgun metagenomics. We found that the urinary microbiome is distinct from nearby sites and is unrelated to stool microbiome. Core urinary microbiome taxa were defined. The first component of weighted unifrac was heritable (18%) as were key taxa (e.g Escherichia-Shigella (A>0.15)). Age, menopausal status, prior UTI and host genetics were top among factors defining the urobiome. Increased composition was associated with older age, contrary to previous findings.
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biorxivpreprint: The urinary tract microbiome in older women exhibits host genetics and environmental influences https://t.co/jSBwKbSuI6 #bioRxiv
biorxiv_micrbio: The urinary tract microbiome in older women exhibits host genetics and environmental influences https://t.co/9EZuyI5W5F #biorxiv_micrbio
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Authors: 8
Total Words: 7147
Unqiue Words: 2827

1.997 Mikeys
#8. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community
Gherman Uritskiy, Michael J Tisza, Diego Gelsinger, Adam Munn, James Taylor, Jocelyne DiRuggiero
Microbial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behavior. This aspect of microbiome function has not been well characterized in natural high-salt environments. To address this knowledge gap, and to build a general framework of relating the genomic and transcriptomic components in a microbiome, we performed a meta-omic survey of extremophile communities inhabiting halite (salt) nodules in the Atacama Desert. We found that the major phyla of this halophilic community have very different levels of total transcriptional activity and that different metabolic pathways were activated in their transcriptomes. We report that a novel Dolichomastix alga - the only eukaryote found in this system - was by far the most active community member. It produced the vast majority of the community's photosynthetic transcripts despite being outnumbered by members of the Cyanobacteria. The divergence in the...
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biorxivpreprint: Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community https://t.co/EXTX7NQI5Y #bioRxiv
biorxiv_micrbio: Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community https://t.co/DVRofCPxRO #biorxiv_micrbio
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Authors: 6
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1.997 Mikeys
#9. Temperature and nutrient gradients correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus
Ruben Props, Vincent J Denef
Most freshwater bacterial communities are characterized by a few dominant taxa, which are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic basis underlying this pattern is limited to a subset of taxa. Here, we investigated the genomic basis that enables Limnohabitans , a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight metagenome assembled genomes (MAGs) from this genus along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be two of the primary...
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1.997 Mikeys
#10. Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in a subarctic alpine heathland
Ingeborg J Klarenberg, Christoph Keuschnig, Ana J. Russi Colmenares, Anne D. Jungblut, Ingibjorg S. Jonsdottir, Oddur Vilhelmsson
Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses, an abundant plant group in many Arctic ecosystems, harbour diverse bacterial communities that are for instance involved in nitrogen fixation. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of the moss microbiome. Here, we study the bacterial community associated with the moss Racomitrium lanuginosum , a common species in the Arctic, in a 20-year in situ warming experiment in an Icelandic heathland. We evaluate changes in bacterial community composition and diversity. Further, we assess the consequences of warming for nifH gene copy numbers and nitrogen fixation rates. Our findings indicate an increase in the relative abundance of Proteobacteria and a decrease in the relative abundance of Cyanobacteria and Acidobacteria with warming. The nifH gene copy number decreases, while the rate of nitrogen fixation is not...
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