March 1st, 2021

God morgon!

Good morning from Sweden. It is hard to believe that it has been a year since the unprecedented happenings of March 2020 but regardless of how we see it, time flies!

The most interesting read of the day is a study that conclusively proves that the oral microbiota is not influenced by your genetics, but by environmental factors. I was intrigued by the use of a video byte, a small video abstract of the paper, which is something new for me. In my opinion, it could very well be the next big thing in academic publishing as it took me just two minutes to understand the whole study! Do check it out!

A promising study is in a preprint where the researchers show that the pre-colonization with a less virulent strain of Clostridioides difficile protects model organisms from subsequent lethal colonization of C. difficile. This has important therapeutic implications in case of nosocomial, antibiotic-promoted diarrhea. Another exciting study shows the influence of gut microbiome on colorectal cancer. The researchers showed that the transplant of ‘good’ microbiota from healthy donors could even reduce the tumorigenesis in the disease models.

Elsewhere in the digest are studies on microbiome of tropical marine sediments, novel proteins from human intestinal microbiome, virulence factors of Trypanosoma brucei, and new therapeutic epitopes in N1 neuraminidase of Influenza virus.

Happy reading!

Bacteria Hysteria

Preprint: Protection from lethal Clostridioides difficile infection via intraspecies competition for co-germinant – Jhansi L. Leslie, et al.

Preprint: Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment – Ana S Almeida, et al.

Preprint: G9a and Sirtuin6 epigenetically modulate host cholesterol accumulation to facilitate mycobacterial survival – Praveen Prakhar, et al.

Preprint: Identification of a chromosomally-encoded sucrose operon-like gene cluster in Vibrio parahaemolyticus strain PH05 isolated from Negros Island, Philippines – Czarina Anne E. De Mesa, et al.

Preprint: Gene flux and acid-imposed selection are the main drivers of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg – Adelumola Oladeine, et al.

Preprint: Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids – Tue Kjærgaard Nielsen, et al.

Preprint: Growth response and recovery of Corynebacterium glutamicum colonies on single-cell level upon defined pH stress pulses – Sarah Täuber, et al.

Preprint: Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis – Dingrong Kang, et al.

Preprint: Calprotectin-mediated zinc chelation inhibits Pseudomonas aeruginosa protease activity in cystic fibrosis sputum – Danielle M. Vermilyea, et al.

General Microbiome

Acquisition of oral microbiota is driven by environment, not host genetics – Chiranjit Mukherjee, et al., Microbiome

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation – Richa Kaushal, et al., Microbiome

The bacterial communities of Alaskan mosses and their contributions to N2-fixation – Hannah Holland-Moritz, et al., Microbiome

Preprint: A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria – Sofiene Seef, et al.

Preprint: Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden, et al.

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome – Hannes Petruschke, et al., Microbiome

Metagenomics and Bioinformatics

Preprint: Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database – Briony A. Jones, et al.

Preprint: Amplicon sequence variants artificially split bacterial genomes into separate clusters – Patrick D. Schloss

Preprint: Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques – Alyssa M Demko, Nastassia V Patin, and Paul R. Jensen.

Viruses

Preprint: The Epstein-Barr virus ubiquitin deconjugase BPLF1 regulates the activity of Topoisomerase II during virus replication – JInlin Li, et al.

Preprint: Novel epitopes of human monoclonal antibodies targeting the influenza virus N1 neuraminidase – Ericka Kirkpatrick Roubidoux, et al.

Others

Preprint: Organotypic endothelial adhesion molecules are key for Trypanosoma brucei tropism and virulence – Mariana De Niz, et al.

February 15th, 2021

God morgon!

Good morning from ice-cold Sweden.

Today’s digest carries interesting preprints on microbiology. I really liked reading the report on a bacteriophage cocktail that kills Listeria without affecting the commensal microbiota and a novel rifampin derivative that is active against doxycycline resistant Francisella. Some preprints highlight the basic biology of bacteria. There is a study on genomic evolution in one of the most important bacterial species – Streptomyces, report on endopeptidases in E. coli, and more reports on methods for studying and annotating antibiotic resistance genes.

Elsewhere in the digest are prediction models for drug interaction iin Tuberculosis, interkingdom biofilms by Candida and Lactobacillus, and microbiome studies on human milk, metazoan-microbe interactions, and some marine microbes.

Finally, there is an interview with Pae-Ji soo, the CEO of Genome and Company who talks about the importance of microbiome in modulating the immunotherapy.

Happy reading!

Bacteria hysteria

Preprint: A bacteriophage cocktail significantly reduces Listeria monocytogenes without deleterious impact on the commensal gut microbiota under simulated gastro-intestinal conditions – Rasmus Riemer Jakobsen, et al.

Preprint: TPR1, a novel rifampin derivative demonstrates efficacy alone and in combination with doxycycline against the NIAID Category A Priority Pathogen F. tularensis – Jason E. Cummings, et al.

Preprint: A nadA mutation confers nicotinic acid auxotrophy in pro-carcinogenic intestinal Escherichia coli NC101 – Lacey R Lopez, et al.

Preprint: A non-adaptive demographic mechanism for genome expansion in Streptomyces – Mallory J Choudoir, et al.

Preprint: Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli – Henri Voedts, et al.

Viruses

Preprint: In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads – Amin Addetia, et al.

Preprint: Methane-derived carbon flow through host-virus trophic networks in soil – Sungeun Lee, et al.

Preprint: Genome sequencing of the bacteriophage CL31 and interaction with the host strain Corynebacterium glutamicum ATCC 13032 – Max Hünnefeld, et al.

General microbiome

Preprint: Chlorine inactivation of Escherichia coli O157:H7 in fresh produce wash process: effectiveness and modeling – Mohammadreza Dehghan Abnavi, et al.

Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis – Meggie Hudspith, et al., Microbiome

Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes – I. Raimundo, et al., Microbiome

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi, et al., Microbiome

Preprint: Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis – Olaf Tyc, et al.

Eukaryotes

Preprint: Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production – Rafael Muñoz-Tamayo, et al.

Preprint: Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis – Vivek Srinivas, et al.

Preprint: Chemical ecology of a tripartite symbiosis – Nicholas C Mucci, et al.

Preprint: Mapping global shifts in Saccharomyces cerevisiae gene expression across asynchronous time trajectories with diffusion maps – Taylor Reiter, et al.

Preprint: Recurrent Vulvovaginal Candidiasis; a dynamic interkingdom biofilm disease of Candida and Lactobacillus
Emily McKloud, et al.

Methods

Preprint: Genie: An interactive real-time simulation for teaching genetic drift – Andreina I Castillo, et al.

Preprint: Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing – Jade Chen, et al.

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li,et al., Microbiome

Others

Microbiome to be game changer in immunotherapy‘ : The Korean Times

December 14th, 2020


God morgon!

Good morning from Sweden.

Mondays are generally light on scientific articles, except for some preprints from Biorxiv. However, the Biorxiv server seems to be down today, so today’s digest mainly focuses on popular News from the world of microbiome.

Often people are confused between ‘probiotics’ and ‘prebiotics’ and their respective benefits. Well, say no more as there is a super nice article explaining both in details! There is an expert interview where the concept of ‘healthy gut microbiome’ is discussed. This might come as a reality check for a lot of people who hold certain beliefs about the microbiome (which aren’t true!).

Also included is an article that talks about the link between gut microbiome and depression. Talking about depression, Vitamin D deficiency is one of the major driving factors of depression. A yet another article reveals how Vit. D absorption is affected by the gut microbiome and how you can maximize your Vit. D absorption (something of utmost importance in dark winters up here!).

I hope you’ll enjoy reading today’s ‘different’ digest!

Microbiome in News

prebiotics vs. probiotics : What is difference — and how to add both to your diet to boost gut health, Broadcast Cover

Using Microbiome Explorer application to analyze amplicon sequencing data, Bioconductor

Gut bacteria linked to endocannabinoid levels and depression, New Atlas

What does a ‘healthy gut microbiome’ look like? In conversation with Danone VP scientific affairs, Dr Miguel Freitas, Food Navigator-USA

You Might Not Absorb as Much Vitamin D as You Think—Here’s How to Maximize the Process, MSN Lifestyle

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