Category Archives: Bacteria Hysteria

December 19, 2025

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Animal microbiome

The innate immune IMD pathway is a key regulator of gut microbiome and metabolic homeostasis in the black tiger shrimp (Penaeus monodon) – Premruethai Supungul – PLOS ONE

Human gut microbiome & nutrition

The evaluation of indoxyl sulfate in the general population in Kanegasaki Iwate: A cross-sectional study (KANEGASAKI study) – Mizuki Hisano – PLOS ONE

The relationship between dietary intake of B vitamins and Helicobacter pylori seropositivity – Yuexia Lu – PLOS ONE

Plant, soil & ecological microbiome

Zinc ion increases the effectiveness of phosphorus in agricultural soils through microbial solubilization – Lanxin Tang – PLOS ONE

Optimizing soil quality and rhizosphere ecology to enhance Annona squamosa yield and quality through water–fertilizer–mulching synergy – Weihua Wang – PLOS ONE

Concentration-dependent effects of fermented spent coffee grounds and contrasting effects of earthworms on growth and phytochemicals in medicinal plant Glechoma longituba – Bing-Nan Zhao – PLOS ONE

Animal experiments (model organisms)

The Drosophila G protein-coupled receptor, GulpR, is essential for lipid mobilization in response to nutrient limitation – Daniela Barraza – PLOS Genetics

High-protein diets reduce plasma pro-inflammatory cytokines following lipopolysaccharide challenge in Swiss Albino mice – Hellen W Kinyi – PLOS ONE

Clinical research & public health

Impact of an integrated intervention package during preconception, pregnancy, and early childhood on inflammation, IGF-1, IGFBP3 during first 6 months of life: Findings from the WINGS randomized controlled trial – Ranadip Chowdhury – PLOS Global Public Health

Lack of association between loneliness, social isolation and inflammation in people living with HIV aged ≥50 years – Jose-Ramon Blanco – PLOS ONE

Effect of obesity and exercise training on circulating lipids in American Indian adolescents – Charles F Hojjat – PLOS ONE

From mental health detention to health systems reform: Co-producing policy and practice recommendations with Black men and their communities – Elaine Craig – PLOS Mental Health

Microbial genetics & bacterial physiology

Whole-genome analysis of Lysinibacillus boronitolerans MSR1: A dairy-isolated multidrug-resistant and non-pathogenic strain – Md Shahedur Rahman – PLOS ONE

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and intra-species cooperation – Ben Vezina – PLOS Biology

Clinical biomarkers & immunology

Blood RNA biomarkers and a point-of-care elastase assay for detecting host immune activation in suspected sepsis – John E Lafleur – PLOS ONE

Multi-omics analysis reveals diagnostic and therapeutic biomarkers for aging phenotypes in ulcerative colitis – Lei Guo – PLOS ONE

Oral health & microbiome

The impact of diet and oral hygiene on dental caries among Turkish children: A cross-sectional study – Ozge Yesildemir – PLOS ONE

Molecular biology & immunity

LIPL-1 and LIPL-2 are TCER-1-regulated lysosomal lipases with distinct roles in immunity and fertility – Laura Bahr – PLOS Genetics

November 27, 2025

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Human gut microbiome

Weifuchun alleviates MNNG-induced chronic atrophic gastritis by improving the gastric and intestinal microbiota homeostasis – Yingying Chen – PLOS ONE

Microbiota-supportive diets and hyperlipidemia: The mediating role of systemic inflammation – Wenjing Wang – PLOS ONE

Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model – Ji-Xin Zhao – PLOS NTDs

Body mass index distinctly modulates the associations between Alistipes and CRP/IL-6 – Lourdes Chero-Sandoval – PLOS ONE

Dogs with advanced myxomatous mitral valve disease have evidence of gastrointestinal bacterial translocation – Maria C Jugan – PLOS ONE

Predicting postoperative constipation in middle-aged and elderly fracture patients using machine learning – Xiaoyan Yang – PLOS ONE

Animal microbiome

Cecal microbiota of broilers responds similarly to black soldier fly larvae fat and conventional fat sources – Muhammad Rumman Aslam – PLOS ONE

Sarcopenia modelling by portal vein ligation inducing hyperammonemia in rats – Maria Nadinskaia – PLOS ONE

Oral / GI cancer microbiome

Serum IgG titer for Fusobacterium nucleatum and clinical outcome in esophageal squamous cell carcinoma – Toru Yoshikawa – PLOS ONE

Phages & bacterial pathogenesis

Structural determinants of SlpA-mediated phage recognition in Clostridioides difficile – Alexia LM Royer – PLOS Pathogens

Disruption of yqhG attenuates virulence in MRSA by compromising membrane stability – Jianhua Liao – PLOS ONE

Host range of generalist and specialist phages in capsule-diverse Klebsiella hosts – Celia Ferriol-González – PLOS Biology

Immunology / human disease

Large-scale seroepidemiology uncovers nephro-urological pathologies with tau autoimmunity – Andreia D Magalhães – PLOS Biology

Plant, soil & ecological microbiome

Root-associated Streptomyces strains enriched during drought reveal diverse functional traits – Citlali Fonseca-Garcia – PLOS Biology

Co-infections shaping Chlamydia pecorum infection outcomes in northern koalas – Yasmine S S Muir – PLOS Pathogens

Trade-offs between yields and sustainability in winter wheat systems under climate change – Jennifer Michel – PLOS Climate

Clinical microbiology

Clinical impact of prophylactic antibiotics in kidney transplantation – Sang Ah Lee – PLOS ONE

Microbial interactions

Veillonella species increase Listeria monocytogenes growth in broth and biofilms – Fanie Shedleur-Bourguignon – PLOS ONE

August 1st, 2022

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God morgon!

Good morning from Sweden.

Today’s digest has studies from diverse topics but the one that caught my attention is a preprint that addresses the controversial question of presence of a ‘normal blood microbiota’ in humans. The authors of this preprint analysed about 10,000 humans samples and provide evidence that there is no core blood microbiota.

A new preprint describes a unique Taleocin (a bacteriocin) from Pseudomonas syringae which defies the convention that bacteriocins have a narrow spectrum. The bacteriocin has a broad range killing activity against agriculturally important pathogens like Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis.

Another preprint reports metabolic interactions responsible for unusually high Iron and lipid content in Geobacter sulfurreducens, a bacterium known iron reducing bacterium in the soil. Another environmental study found that human pathogens are the major carriers of antibiotic resistance genes in the Yangtze river – one of the longest in the world. This is in contrast to prevalent belief that conventional supercarriers are Enterococcus spp. and other fecal indicator bacteria.

Elsewhere in the digest is a preprint from my previous lab where my old colleagues have reported a small RNA and metal dependent mechanism that regulates the survival of Acinetobacter baumannii under oxidative stress.

As a bonus, there is a super intriguing preprint where the authors have actually provided evidence that coming up with creative and funny titles for your papers can help them gain more visibility and citations! So, all of you writing an article or planning to write one soon, this is a great tip!

I hope you will enjoy reading today’s digest and have a great week ahead!

Human gut

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C. Holmes, et al., Microbiome

Near-sterile sites

Preprint: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan, et al.

Water microbiome

Supercarriers of antibiotic resistome in a world’s large river – Jiawen Wang, et al., Microbiome

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater – Jingli Liu, et al., Microbiome

Community structure of coral microbiomes is dependent on host morphology – Kathleen M. Morrow, et al., Microbiome

Preprint: The impact of primary colonizers on the community composition of river biofilm – Roshan Angoshtari, et al.

Soil microbiome

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity – Xingyu Ma, et al., Microbiome

Animal microbiome

Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs – Xuan Zhao, et al., Microbiome

Preprint: The differing roles of flavins and quinones in extracellular electron transfer in Lactiplantibacillus plantarum – Joe Gregory Tolar, et al.

Bacteria Hysteria

Preprint: Interspecies Killing Activity of Pseudomonas syringae Tailocins – Savannah L Weaver, et al.

Preprint: Enhanced production of natural shiga toxin by overexpressing A subunit of Stx2e in Stx2e-producing Escherichia coli isolated in South Korea – Jin Hur, et al.

Preprint: Geobacter sulfurreducens′ unique metabolism results in cells with a high iron and lipid content – Ethan T Howley, et al.

Preprint: Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium – Madan Junghare

Preprint: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated suppression of type VI secretion system – Somok Bhowmik, et al.

Techniques

Preprint: Programmable acetylation modification of bacterial proteins by a Cas12a-guided acetyltransferase – Liu yanqiang, et al.

Fun

Preprint: If this title is funny, will you cite me? Citation impacts of humour and other features of article titles in ecology and evolution – Stephen B Heard, et al.

September 21st, 2020

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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

July 1, 2020

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Greetings Everyone,
I want to began the month of July on a note that diversity is the basis for life. I can’t think of anything better to teach us about diversity, co-existence, and evolution than the fascinating Microbiome.
The microbiome affects us right from our birth till the end affecting our mental as well as physical health. The microbiome exhibits all sorts of differences in shape, size, color, metabolic functions in order to sustain life.
Much to learn from these tiny beings!!!!
Today’s Digest comprises of some interesting studies about effect of microbiome on chemotherapy and studies on tumor microbiome. It also includes articles exploring genetics of gut microbiome and the role of microbiome in inflammatory bowel disease. Additionally has a news article about taking microbiome therapies to clinical trials.
Hope you enjoy reading today’s digest!!
“Life on earth is such a good story you cannot afford to miss the beginning… Beneath our superficial differences we are all of us walking communities of bacteria. The world shimmers, a pointillist landscape made of tiny living beings”. – Lynn Margulis

General microbiome
Human Microbiota and Effectiveness of Cancer Chemotherapy – Shvets et al – Experimental Oncology

Immunity to commensal skin fungi promotes psoriasiform skin inflammation – Hurabielle et al – PNAS

Human Tumor microbiome
*Perspective: Probing the tumor micro(b)environment – Atreya et al – Science

Human Eye microbiome
Review: Current Knowledge on the Human Eye Microbiome: A Systematic Review of Available Amplicon and Metagenomic Sequencing Data – Delbeke et al – Acta Ophthalmologica

Human nearly-sterile sites (blood, organs, brain)
Blood Bacterial Profiles Associated with HIV Infection and Immune Recovery – Serranno-Villar et al – The Journal of Infectious Diseases

Human gut microbiome
*Genetics of human gut microbiome composition – Kurilshikov et al – bioRxiv

Review: The microbiome in inflammatory bowel diseases: from pathogenesis to therapy – Liu et al – Protein&Cell

Built environment
Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al – bioRxiv

Food microbiology
Food and mood: how do diet and nutrition affect mental wellbeing? – Firth et al – BMJ

Bioinformatics
DRAM for distilling microbial metabolism to automate the curation of microbiome function – Shaffer et al – bioRxiv

Techniques
MetaRibo-Seq measures translation in microbiomes – Fremin et al – Nature Communications

Microbes on the market
Enterome Secures €46M to Take Microbiome Therapies to Clinical Trials – Helen Albert – Labiotech.eu

Human Microbiome Therapeutics Market Research: Global Status & Forecast by Geography, Type & Application (2016-2026)

June 20th, 2020

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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

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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

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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 6, 2020

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God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!

COVID19

Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Emily K. Mantlo, et al.

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.

Techniques

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.

Bioinformatics

Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!

November 29, 2018

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Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice – Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition