October 5th, 2020


God morgon!

Good morning from Sweden.

Today’s digest starts with a super interesting preprint on COVID-19 where the researchers have shown that anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus. As if COVID-19 wasn’t dangerous enough, its treatment is now even more dangerous!

New research has revealed numerous genera of bacteria associated with Amoebozoa, which haven’t been looked into; polyamines as new substrates for a previously known efflux pump in Acinetobacter; genomic differences between the influenza viruses causing infections of different severity; and novel interactions between mycorrhizal fungi and plants.

Hope you’ll enjoy today’s digest!

COVID-19

Preprint: SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus – Jungang Chen, et al.

Bacteria Hysteria

Preprint: Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP317-326 – Maria Georgieva, et al.

Preprint: Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System – Heidi MT Kunttu, et al.

Preprint: ROS-dependent innate immune mechanisms control Staphylococcus aureus MRSA virulence in the Drosophila larval model – Elodie Ramond, et al.

Preprint: Transposon-insertion sequencing in a clinical isolate of Legionella pneumophila identifies essential genes and determinants of natural transformation – Léo Hardy, et al.

Preprint: Spermidine and spermine are the natural substrates of the Acinetobacter baumannii AmvA multidrug efflux pump – Francesca L. Short, et al.

Gut Microbiome

Preprint: Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Eric Daniel Adams, et al.

Preprint: Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan, et al.

Preprint: Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa – Yonas I. Tekle, et al.

β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice – Hongli Shi, et al., Microbiome

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato, et al., Microbiome

Plants

Preprint: Comparative analysis of temporal transcriptome reveals the relationship between pectin degradation and pathogenicity of defoliating Verticillium dahliae to Upland cotton (Gossypium hirsutum) – Fan Zhang, et al.

Preprint: Silencing of ATP synthase β reduces phytoplasma multiplication in the leafhopper vector Euscelidius variegatus – Luciana Galetto, et al.

Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences – Yuji Jiang, et al., Microbiome

Preprint: Characterization of Met25 as a Color Associated Genetic Marker in Yarrowia lipolytica – Harley Edwards, et al.

General Microbiome

Preprint: Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean – Mar Benavides, et al.

Preprint: Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin – Sabyasachi Bhattacharya, et al.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Shawn P. Brown, et al., Microbiome

Viruses

Preprint: A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the E protein: a possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan – Tomohiro Kotaki, et al.

Preprint: Differential Disease Severity and Whole Genome Sequence Analysis for Human Influenza A/H1N1pdm Virus in 2015-2016 Influenza Season – Hsuan Liu, et al.

Viral ecogenomics across the Porifera – Cecília Pascelli, et al., Microbiome

Infections

Preprint: A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis – Andrew O’Connor, et al.

Preprint: Modulation of early host innate immune response by a Fowlpox virus (FWPV) lateral body protein – Efstathios S Giotis, et al.

Techniques

Preprint: Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung, et al.

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin, et al., Microbiome

September 21st, 2020

God morgon!

Good morning from Sweden. It’s Monday, beginning of a new week and today’s digest carries a lot of preprints with interesting information.

As ususal, new knowledge about COVID-19 keeps pouring in. A library of 1200 small molecules was screened to reveal at least 20 FDA-approved small molecules that can enhance the antiviral activity of remdesivir. A human enzyme was also shown to be involved in antiviral defences. A new preprint also revealed some modifications in the SARS-CoV-2 spike protein that can increase vaccine efficacy.

Continuing with viruses, new preprint report an improved Zika vaccine, a basic study exploring reverse transcription and thereby developing a better system to study anti-HIV drugs, and a new detailed protocol for enriching viromes in water samples.

Also in today’s digest are some preprints on basic bacteriology with reports on (p)ppGpp and persister cells, Streptococcal membranes, secretory products and their role in Listeria virulence, and efflux pumps in Burkholderia.

Apart from these, there are, coincidentally, two reports on microbial diversity of the waters of Shark Bay, Australia, algal diversity in corals, a relationship between termite gut-microbiota and changes in temperature, and the role of gut microbiota in possibly affecting the sexual dimorphism in susceptibility to diseases.

Hope you enjoy the collection!

COVID-19

Preprint: Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells – Xammy Nguyenla, et al.

Preprint: A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro – Tianshu Xiao, et al.

Preprint: Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples – Vinod Kumar, et al.

Preprint: Introduction of two prolines and removal of the polybasic cleavage site leads to optimal efficacy of a recombinant spike based SARS-CoV-2 vaccine in the mouse model – Fatima Amanat, et al.

Viruses

Preprint: Measles-based Zika vaccine induces long-term immunity and requires NS1 antibodies to protect the female reproductive tract in the mouse model of ZIKA – Drishya Kurup, et al.

Preprint: Cocculus hirsutus-derived phytopharmaceutical drug has potent anti-dengue activity – Ankur Poddar, et al.

Preprint: Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication – Benjamin M. Akiyama, et al.

Preprint: Chemical Stabilization of the HIV-1 Capsid Results in Efficient HIV-1 Reverse Transcription in vitro – Jordan Jennings, et al.

Preprint: Life cycle process dependencies of positive-sense RNA viruses suggest strategies for inhibiting productive cellular infection – Harsh Chhajer, et al.

Preprint: Zika virus NS3 protease and its cellular substrates – Agnieszka Dabrowska, et al.

Preprint: A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples – Federica Pinto, et al.

Preprint: Matrix metalloproteinases and tissue inhibitors of metalloproteinases in murine coronavirus-induced neuroinflammation – Sourodip Sengupta, et al.

Bacteria Hysteria

Preprint: The generation of persister cells is regulated at the initiation of translation by (p)ppGpp – Roberto C. Molina-Quiroz and Andrew Camilli.

Preprint: Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse – Mikkel Skjoldan Svenningsen, et al.

Preprint: Slipped strand mispairing in the gene encoding cell wall associated sialidase NanH3 in Gardnerella spp – Shakya P. Kurukulasuriya, et al.

Preprint: Membrane linkage of a Streptococcus pneumoniae Wzy capsular polysaccharide occurs through an acylglycerol – Thomas R. Larson and Janet Yother.

Preprint: Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells – Caroline Peron-Cane, et al.

Preprint: Burkholderia collagen-like protein 8, Bucl8, is a unique outer membrane component of a tetrapartite efflux pump in Burkholderia pseudomallei and Burkholderia mallei – Megan E Grund, et al.

Preprint: Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis – Anahita Bakochi, et al.

Preprint: Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types – Thomas Edwards, et al.

Preprint: Analysis of beta-lactam heteroresistance in CRE suggests a stage in the spectrum of antibiotic resistance – Victor I Band and David S Weiss

Preprint: Mechanism of selectivity reveals novel antifolate drug interactions – Shannon Lynn Kordus, et al.

Preprint: Identification of trans-AT polyketide clusters in two marine bacteria reveals cryptic similarities between distinct symbiosis factors – Dina Kačar, et al.

Preprint: Heterologous production of 1-tuberculosinyladenosine in Mycobacterium kansasii models pathoevolution towards the transcellular lifestyle of Mycobacterium tuberculosis – Marwan Ghanem, et al.

General Microbiome

Preprint: Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut – Jacobo de la Cuesta-Zuluaga, et al.

Preprint: Metagenomic insights into ecosystem function in the microbial mats of Blue Holes, Shark Bay – Gareth S Kindler, et al.

Preprint: Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods – Gina R Lewin, et al.

Preprint: Functional diversity of microboring Ostreobium algae isolated from corals – Anaïs Massé, et al.

Preprint: Experimental warming reduces gut prokaryotic diversity, survival and thermal tolerance of the eastern subterranean termite, Reticulitermes flavipes (Kollar) – Rachel A Arango, et al.

Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status – Jordi Mayneris-Perxachs, et al., Microbiome

Techniques/Models

Preprint: Cre/LoxP-HBV plasmids generating recombinant covalently closed circular DNA genome upon transfection – Robert L. Kruse, et al.

Preprint: A Novel DNA Chromatography Method to Distinguish M. abscessus Subspecies and Macrolide Susceptibility – Mitsunori Yoshida, et al.

Others

Preprint: Phytophthora sojae effector Avr1d functions as E2 competitor and inhibits ubiquitination activity of GmPUB13 to facilitate infection – Yachun Lin, et al.

Preprint: A Volatile Signal Controls Virulence in the Plant Pathogen Pseudomonas syringae pv. syringae and a Strategy for Infection Control in Organic Farming – Simon Sieber, et al.

Preprint: Schistosoma mansoni lysine specific demethylase 1 (SmLSD1) is a druggable target involved in parasite survival, oviposition and stem cell proliferation – G. Padalino, et al.

Preprint: Alterations to the cardiac metabolome induced by chronic T. cruzi infection relate to the degree of cardiac pathology – Kristyn Hoffman, et al.

Preprint: Remarkable recent changes in genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici – Christopher Stephens, et al.

Microbes in News

Soon-to-be-launched microbiome concept symbiome raises $15mm – Beauty Matters

Finch closes $90 million series d to advance C. difficile infection product – Pharma Live

September 7th, 2020

God morgon!

Good morning from Sweden. Today’s digest is a loaded one with a lot of new preprints and news from the world of microbiology.

As someone who suffers from allergic rhinitis my mind was blown when I read the article that linked gut microbiota to allergic rhinitis! I am waiting for someone to come up with a gut microflora based treatment now! Further in the area of microbiome are preprints on assessment of antibiotic use in neonates and barcoding of about 1000 new marine yeast isolates.

A new preprint details the mechanism of action of a very effective new antibiotic armeniaspirol against Gram positive bacteria. Yet another preprint describes the potent antimycobaterial activity of synthetic Azetidines derivatives, which could be a great tool in our fight against tuberculosis. Further in bacteriology are preprints providing new information about host-pathogen interactions during Helicobacter infections, dynamics in persisting and resuscitating bacteria, RNA metabolism and metabolic homeostasis in bacteria.

A super interesting preprint describes a new form of on-chip microscopy and I must confess that the authors did a great job at giving their manuscript a catchy, short and yet informative title!

Bioinformatic studies using thousands of nCoV genomes have unearthed some mutations that might be responsible for its human adaptation (although computational studies without any experimental biological evidence are not my favourite, it might provide a starting point for scientists interested in COVID19.

There are a lot of more interesting articles and I wish I could write about all of them! I hope you will enjoy today’s selection.

COVID-19

Preprint: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe – Weitao Sun

Preprint: Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus – Majid Vahed, et al.

Preprint: Development of SARS-CoV-2 Nucleocapsid Specific Monoclonal Antibodies – James S. Terry, et al.

Preprint: A Mental Health Paradox: Mental health was both a motivator and barrier to physical activity during the COVID-19 pandemic – Maryam Marashi, et al.

Bacteria Hysteria

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu, et al., Microbiome

Preprint: Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria – Puneet Labana, et al.

Preprint: Effect of polyethylene glycol on growth of Escherichia coli DH5α and Bacillus subtilis NRS-762 – Wenfa Ng

Preprint: Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis – Larissa Krüger, et al.

Preprint: Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage – Nikola Palevich, et al.

Preprint: Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment: a randomized trial of preterm infants – Jordan T. Russell, et al.

Preprint: Azetidines kill Mycobacterium tuberculosis without detectable resistance by blocking mycolate assembly – Alice Lanne, et al.

Preprint: Proteome dynamics in persisting and resuscitating bacterial cells – Maja Semanjski, et al.

Preprint: Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis – Roberto E. Bruna, et al.

Preprint: RecA levels modulate biofilm development in Acinetobacter baumannii – Carly Ching, et al.

Preprint: Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate – Yusuke Himeoka, et al.

General microbiome

Gut microbial characteristics of adult patients with allergy rhinitis – Libing Zhu, et al., Microbial Cell Factories

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak, et al., Microbiome

Preprint: Soil characteristics constrain the response of bacterial and fungal communities and hydrocarbon degradation genes to phenanthrene soil contamination and phytoremediation with poplars – Sara Correa-García, et al.

Preprint: Microbial bioprospecting for lignocellulose degradation at a unique Greek environment – Daphne N. Georgiadou, et al.

Preprint: DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species – Chinnamani PrasannaKumar, et al.

Viruses

Preprint: Mammalian ANP32A and ANP32B proteins drive alternative avian influenza virus polymerase adaptations – Thomas. P. Peacock, et al.

Preprint: Development of Resistance to 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine (EFdA) by Wild-Type and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1 – Maria E Cilento, et al.

Host-pathogen interactions

Preprint: NHR-49/PPAR-α and HLH-30/TFEB promote C. elegans host defense via a flavin-containing monooxygenase – Khursheed A. Wani, at al.

Preprint: Role of ERK activation in H. pylori-induced disruption of cell-cell tight junctions – Amita Sekar and Bow Ho

Preprint: Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response – Brigitte E Martin, et al.

Preprint: Non-permissive human conventional CD1c+ dendritic cells enable trans-infection of human primary renal tubular epithelial cells and protect BK polyomavirus from neutralization – Mathieu Sikorski, et al.

Techniques

Preprint: Nanoscopy on the Chea(i)p – Benedict Diederich, et al.

Preprint: Visualizing Borrelia burgdorferi infection using a small molecule imaging probe – Madeline G Sell, et al.

Microbiology in News

Malibu Microbiome Meeting Virtual Prelude Shares New Data – PR Newswire

Human Microbiome-Based Drugs And Diagnostics Market An Insight On the Important Factors and Trends Influencing the Market – Daily Research Chronicle

Autism and the Microbiome – The New Indian Express

August 24th, 2020

God morgon!

Good morning from Sweden.

I am sure there are a lot of labs and scientists with interesting therapeutic options against COVID19, but unable to do so due to lack of BSL-3 facilities. Good news for them as today’s digest carries a preprint where some researchers show that a recombinant vesicular stomatitis virus expressing nCoV spike protein can be used to evaluate the potential of anti-spike antibodies. They designed a specific assay which could be modified to work out for evaluation of other therapeutics. Continuing with viruses, there is another preprint that delineates a new strategy to design effective vaccines against Ebola virus.

New research published in Microbiome journal describes the effect of antimicrobials on salivary microbiota and how gut microbiota may be implicated in regulating autism-like behaviour through vitamin B6 homoeostasis.

Elsewhere in the digest is new research featuring a new technique ‘Protoblock’ for increasing reproducibility in pathology samples, biocontrol of plant disease using bacteria, on-site detection of Genus Clavibacter, and the basis of cell polarity in bacteria.

Happy reading and have a great week!

Preprint: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein – Hideki Tani, et al.

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition – Sajan C. Raju, et al, Microbiome

The gut microbiota regulates autism-like behavior by mediating vitamin B6 homeostasis in EphB6-deficient mice – Ying Li, et al, Microbiome

Preprint: Scaffold-scaffold interactions regulate cell polarity in a bacterium – Wei Zhao, et al.

Preprint: Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines – Linling He, et al.

Preprint: Multiplex recombinase polymerase amplification (RPA) assay developed using unique genomic regions and coupled with a lateral flow device for rapid on-site detection of genus Clavibacter and C. nebraskensis – Adriana Larrea-Sarmiento, et al.

Preprint: Evaluation of the efficacy of some PGPR bacteria in controlling Fusarium wilt disease Fusarium oxysporum f.sp. lycopersici on the tomato plant – Halima Z Hussein and Shaker I Al-Dulaimi.

Preprint: Mutually Beneficial Symbiosis Between Human and Gut-Dominant Bacteroides Species Through Bacterial Assimilation of Host Mucosubstances – Masahiro Sato

Protoblock – A biological standard for formalin fixed samples – Yensi Flores Bueso, et al, Microbiome

Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate – Nguyen K. Nguyen, et al, Microbiome

August 10th, 2020

God morgon!

Good morning from Sweden. Today’s digest is a light one but carries a preprint with some very important findings. The study has suggested that the nCoV can potentially hijack the immune system completely by infecting the lymphocytes. This might lead to impaired antibody and T-cell response, something that could have a serious implication on the success of the much-awaited vaccine. (Unfortunately, for some unknown reasons, the PDF of the preprint is inaccessible to me! Let me know down in the comments if you are able to download it.)

A new paper in BMC microbiome shows a correlation between the indoor dust microbiota and the microbiota of infant airways. A classic example of how our environment impacts our health.  There is another interesting preprint where the authors show that a fungus alters its virulence when it is challenged by predatory amoebae. Perhaps the amoeba challenge selects for the warrior mutants which then carry on their warring ways!

Elsewhere in the digest is a preprint where Plasmodium knowlesi was used as a model to successfully determine new vaccine targets against more dangerous Plasmodium vivax, a paper detailing the effect of polar light cycles on the Antarctic lake microbiome, and identification of haloarchael species in Korean gut microbiota.

COVID-19

Preprint: Infection of human lymphomononuclear cells by SARS-CoV-2 – Marjorie C Pontelli, et al.

General Microbiology

Preprint: Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence – Man Shun Fu, et al.

Preprint: Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates – Duncan N Ndegwa, et al.

General microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar, et al. – Microbiome

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota – Shashank Gupta, et al. – Microbiome

Archaea/Gut microbiota

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Joon Yong Kim, et al. – Microbiome

Techniques

Preprint: Successful introduction of the Colour Test into inexperienced settings – Kadri Klaos

Zoom Seminar

How a healthy gut microbe affects your whole body? – Karen Ranzi, Holistic Health Coach, Award-Winning Author, Motivational Speaker, Natural Foods Chef, Speech and Feeding Therapist (phew!)

July 6, 2020

God morgon!

Good morning from Sweden. Another new week and another new digest! Today’s digest is very light with only a few articles. There is an interesting preprint which reports that the SARS-CoV-2 spike protein variant D614G leads to increased infectivity and the virus might have acquired this mutation during human-to-human transmission as this mutation is not seen in the original virus that infects the non-human hosts. This might be the reason why about 97% of the nCoV19 isolates have this mutation. However, the good news is that the neutralizing antibodies against the wildtype virus still retain the ability to target this mutant virus. Another interesting commentary published in Microbiome journal revisits important concepts in microbiome biology and is a must-read for all the microbiome enthusiasts. Elsewhere in the digest is a study on microbial succession in deep-sea hydrothermal vents, microbial communities of small brown planthopper (Laodelphax striatellus) and Shrimp (Litopenaeus vannamei), and thermophilic digestion of biowaste.

Happy reading and have a great week!

COVID 19

Preprint: SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain – Leonid Yurkovetskiy, et al.

General Microbiome

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle – Yanting Wang, et al. – Microbiome

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste – Stefan Dyksma, et al. – Microbiome

Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations – Xing-Zhi Duan, et al. – Microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg, et al. – Microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Jialin Hou, et al. – Microbiome

 

June 20th, 2020

Glad midsommar!

Happy midsummer to everyone from Sweden. Today’s digest is heavy on the preprints with a couple of thought-provoking editorials from the journal Nature. You will notice a lot of articles related to COVID-19. There is an interesting study that proposes the use of dogs and their sensory powers to detect CoV infections. More importantly, a preprint discusses the use of a tyrosine kinase as a potential drug and another preprint discusses the results of a massive FDA-approved drug repurposing screen for COVID. Also in the digest is an article where the researchers have shown that the gut microbiome produces neurotransmitters and another article that explains how Streptomyces spores hitchhike. Another article, although not related to our general theme, is super interesting as well. A group of scientists have proposed that the first egg of the dinosaurs was probably soft-shelled and not like the hard eggs we imagined all this time!

I am sorry for doing a lousy job today at providing a proper context and some informative introduction to today’s digest as it is the most awaited Midsommar holiday and the barbecue is calling! I hope everyone is enjoying the summer. Make sure to follow social distancing guidelines!

COVID-19

Preprint: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 – Nirmitee Sanjay Mulgaonkar, et al.

Preprint: Variant analysis of SARS-CoV-2 strains in Middle Eastern countries – Khalid M Bindayna and Shane Crinion

Preprint: Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance – Eric Dumonteil and Claudia Herrera

Preprint: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters – Rebecca Brocato, et al.

Preprint: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States – Ryan P McNamara, et al.

Preprint: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window – Duarte Gouveia, et al.

Preprint: A single dose of recombinant VSV-∆G-spike vaccine provides protection against SARS-CoV-2 challenge – Yfat Yahalom-Ronen, et al.

Preprint: Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine – Suzanne JF Kaptein, et al.

Preprint: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 – Mark Dittmar, et al.

Preprint: Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs – Omar Vesga, et al.

Preprint: Evaluation of the performance of SARS-CoV-2 serological tools and their positioning in COVID-19 diagnostic strategies. – Aurélie Velay, et al.

General Microbiome

Preprint: Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome – Deborah Iwanowicz, et al.

Preprint: Hi-C deconvolution of a textile-dye degrader microbiome reveals novel taxonomic landscapes and link phenotypic potential to individual genomes – Ayixon Sanchez-Reyes, et al.

A metabolic pathway for bile acid dehydroxylation by the gut microbiome – Masanori Funabashi, et al. – Nature

A neurotransmitter produced by gut bacteria modulates host sensory behaviour – Michael P. O’Donnell, et al. – Nature

Proteome

Preprint: Novel functional insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies – Lisette Meerstein-Kessel, et al.

Bacteria

Preprint: Conjugal DNA transfer in the maternally inherited symbiont of tsetse flies Sodalis glossinidius – Christopher G Kendra, et al.

Preprint: Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination. – John M. Atack, et al.

Preprint: The role of LmeA, a mycobacterial periplasmic protein, in stabilizing the mannosyltransferase MptA and its product lipomannan under stress – Kathryn C Rahlwes, et al.

Preprint: Microbial piggy-back: how Streptomyces spores are transported by motile soil bacteria – Alise R. Muok, et al.

Viruses

Preprint: Herbivore-induced activation of viral phosphatase disarms plant antiviral immunities for pathogen transmission – Pingzhi Zhao, et al.

Preprint: Quantifying the acquisition and retention of lumpy skin disease virus by haematophagus insects and the implications for transmission and control – Beatriz Sanz-Bernardo, et al.

Preprint: Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) – Benjamin C. Nick, et al.

Preprint: A sweep of earth’s virome reveals host-guided viral protein structural mimicry; with implications for human disease – Gorka Lasso, et al.

Others

The first dinosaur egg was soft – Mark A. Norell, et al. – Nature

Junior researchers hit by coronavirus-triggered hiring freezes – Chris Woolston – Nature

Peer review should be an honest, but collegial, conversation Nature

June 1, 2020

God morgon!

Good morning from Sweden. It’s a new week and a new month! I hope everyone is doing good and staying healthy during these tough times. Like the tradition, today’s digest opens with COVID 19 related articles. There is an interesting Q&A article that provides a lot of important information. There is an article that focused on the disease progression and recovery from COVID in children and found out that Computerized Tomography (CT) may not be the best tool when it comes to analyzing COVID in children. Apart form COVID 19, there is also some new interesting information from the structure of Type-IV pilus. Elsewhere in the digest is an article on an easy to use toolkit for microbiome analysis and development of a new path-breaking point-of-care system for rapid detection of mycobacteria.

Hope you’ll enjoy and learn something new from today’s digest!

COVID 19

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher and David Heymann – BMC Medicine

Preprint: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes – Ching-Lin Hsieh, et al.

A single-center, retrospective study of COVID-19 features in children: a descriptive investigation – Huijing Ma, et al. – BMC Medicine

Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK – Christopher I. Jarvis, et al. – BMC Medicine

General Microbiome

Preprint: Microbial strategies for survival in the glass sponge Vazella pourtalesii – Kristina Bayer, et al.

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria – Xingxing Jian, et al. – Microbiome

Viruses

Preprint: Oropouche virus glycoprotein topology and cellular requirements for virus-like particle assembly – Natalia da silva barbosa, et al.

Bacteria

Preprint: Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis – Natalia Díaz-Garrido, et al.

Preprint: Investigations of dimethylglycine (DMG), glycine betaine and ectoine uptake by a BCCT family transporter with broad substrate specificity in Vibrio species – Gwen Gregory, et al.

Preprint: TsaP binds PilQ and is involved in cyclic di-GMP signaling – Matthew McCallum, et al.

Preprint: SoxS represses flagellar gene expression through RflP in Salmonella enterica Serovar Typhimurium – Srinivas S Thota, et al.

Preprint: Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes – Mireille Kamariza, et al.

Techniques

Preprint: animalcules: Interactive Microbiome Analytics 1 and Visualization in R – W. Evan Johnson, et al.

May 18, 2020

God morgon!

Good morning from Sweden. It’s Monday and the beginning of another week. I am quite excited to write today’s digest because there is a super impressive paper that concerns my area of research. Research efforts in Shigella infections have always suffered from the lack of a mouse model of infection. This notorious bacterium causes enteric infections only in humans and all the infection models, that have been in use so far,  are not physiologically that relevant. It was extremely thrilling to read the development of a mouse model that replicates the typical features of human infections. Talking about infection models, there is another interesting development. A group of researchers has reported an African green monkey model for CoViD-19. This is an important development for clinical assessment of potential vaccine and drug candidates against nCoV-19.

Speaking of vaccines, another group has reported a Neisseria meningitidis outer membrane vesicle (OMV) based vaccine that provides cross-species protection against Neisseria gonorrhoeae. This report assumes great importance when you consider the fact that no Neisseria gonorrhoeae vaccine has entered clinical testing for the past 30 years! In addition to this, there is a structural study of budding in Cryptococcus neoformans that has some really beautiful pictures like this one:

Screenshot 2020-05-18 at 14.57.43

Elsewhere in the digest are some interesting reports on the virulence of a root pathogen, Fusarium; metagenomic identification of diverse viruses; a potent mycobacteriophage; and commentary on Coronaviruses as pathogens responsible for pandemics.

Hope you enjoy today’s selection and have a great week!

COVID-19

Preprint: Establishment of an African green monkey model for COVID-19 – Courtney B. Woolsey, et al.

Preprint: Coronavirus, as a source of pandemic pathogens – Tomokazu Konishi

Bacteria Hysteria

Preprint: NAIP-NLRC4-deficient mice are susceptible to shigellosis – Patrick S Mitchell, et al.

Preprint: The serogroup B meningococcal outer membrane vesicle-based vaccine 4CMenB induces cross-species protection against Neisseria gonorrhoeae – Isabelle Leduc, et al.

Preprint: Antimycobacterial potential of Mycobacteriophage under pathophysiological conditions – Yeswanth C Kalapala, et al.

Preprint: A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex – Paul D Caccamo, et al.

Preprint: Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes – Kathirvel Kandasamy, et al.

Human gut

Preprint: Higher prevalence of Bacteroides fragilis in Crohn’s disease exacerbations and strain-dependent increase of epithelial resistance – Heike E.F. Becker, et al.

Fungi

Preprint: Let it bud: an ultrastructural study of Cryptococcus neoformans surface during budding events – Glauber R. de S. Araujo, et al.

Methods

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa, et al. – Microbiome

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh and Ni Zhao – Microbiome

Metagenomics

Preprint: Metagenomic identification of diverse animal hepaciviruses and pegiviruses– Ashleigh F. Porter, et al.

Transcriptomics

Preprint: Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen – Yi Ding, et al.

Microbes in the News

Living on The Space Station Leaves a Microbial ‘Fingerprint’ on Astronauts – Science Alert

What are the best foods to increase happiness? – Eastern Daily Press

April 20, 2020

God morgon!

Good morning from Sweden. To all my friends who have lost the track of time during the quarantine, it is Monday and the beginning of a new week. Today’s digest is a very light one. However, it carries a super interesting preprint that studies the impact of the pandemic on publication speed of different medical journals. The study reports that, on average, the COVID-19 related papers were expedited through the peer-review process at a 49% (up to 80% in case of certain journals) higher pace than the mean pre-pandemic publishing speed (Yes, there is a pre-pandemic and, possibly, a post-pandemic era now). Although this is a controversial topic, I guess the preprint did a very good job of discussing the reasons behind and impact of accelerated publishing.

In my personal opinion, it is great to be able to get valuable scientific information as soon as it is produced. However, as the paper points out, there has to be some sort of trade-off between the quality of a publication and the time taken by the peer-review process. It could be argued that the quarantine measures might have made it easier for some reviewers to focus their attention on the peer-review, making it faster, but there is no information on ‘who’ reviewed these papers. Also, the article highlights what a lot of scholars have been warning about – the amount of post-publishing corrections that these papers would require (more work for Ms Bik!).

What do you think could be the reasons behind this unprecedented celerity of publishing? Could it be the availability of more spare time to review papers? or could this be an instance of politicization of science (as someone pointed out in the comments section of the article)? What could be the impact of this swiftness, both positive and negative, on the scientific realm? Would it be possible, or advisable, to keep up this trend of swift publishing in the post-pandemic era? Let’s discuss in the comments section.

Apart from this highly thought-provoking article, there is another interesting article on the identification of bacterial strains that may promote maize (corn, for my American friends) growth in chilling conditions.

There is another interesting article that tries to establish a link between the gut microbiome and memory. The study focused on microbiome-specific genetic and metabolomic changes that may impact memory. The study was performed in mice.

Enjoy the articles, have a great week, and stay safe!

COVID 19

Preprint: Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19 – Serge P.J.M. Horbach

Preprint: Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity – Collin D Heer, et al.

Animal microbiome

Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao, et al. – Microbiome

Plant root-soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx, et al. – Microbiome

Microbial interactions

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Michael W. Henson, et al.