August 15th, 2022

God morgon!

Good morning from Sweden. Today’s digest is a bag full of articles, mostly preprints, from various fields. A newly published article reports that non-antibiotics, carbamazepine, ibuprofen, naproxen and propranolol, affect the horiontal gene transfer (HGT) and promote sharing of plasmids that encode antibiotic resistance genes. This is an important conclusion as so far we were bothered only about antibiotics but now there is evidence that even non-antibiotics can promote antimicrobial resistance.

Staying with antibiotics, a new preprint reports Ruthenium complexes as potent antibacterial compounds against clinical strains of Pseudomonas aeruginosa. The group was able to demonstrate the mode of action of these compounds and also find mutations that might promote supressor phenotype. These compounds also show synergism with Rifampicin, a known antibiotic. Another preprint about P. aeruginosa reports that the bacterium carries multitude of phage resistance mechanisms to fend of bacteriophages. These mechanisms determine the host specificity of phages as individual resistance mechanism only provide resistance against specific phages. This can be a vital information for planning phage therapies.

Elsewhere in the digest are reports on correlation between the presence of certain microbial species with the presence of Legionella in selected EU cities, importance of gut microbiota on glucose metabolism in offspring, and how the climate change induced influx of Atlantic waters in Arctic affects the microbial diversity.

In the end, there is a special report on how certain dietary compounds can alter the micrbes in our food and result in changes to our food. The scientists have proposed a new field of research – nutrifermentics. They report how Benzoic acid, a common food additive, can induce epigenetic changes in Saccharomyces cerevisiae that alter the characteristic of wine. This has important implications in strain developement where deliberate genetic modifications may be avoided by inducing epigenetic changes using such additives.

I hope you will enjoy reading today’s digest. Have a great week!

Water microbiome

Preprint: Genome-resolved community structure and function of freshwater bacteria at a continental scale – Rebecca E. Garner, et al.

Preprint: Bacterial communities of premise plumbing systems in four European cities, and their association with culturable Legionella – Maria Scaturro, et al.

Preprint: Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities – Taylor Priest, et al.

Bacteria Hysteria

Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level – Yue Wang, et al. Microbiome

Preprint: Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal – an Effective Poultry Disease Surveillance Tool – Shreeya Sharma

Preprint: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections – Désirée A. Schmitz, Richard C. Allen, and Rolf Kümmerli

Preprint: Growth arrest of Staphylococcus aureus induces daptomycin tolerance via cell wall remodelling – Elizabeth V. K. Ledger and Andrew M. Edwards

Preprint: Polynuclear ruthenium complexes are effective antibiotics against Pseudomonas aeruginosa – Brent S. Weber, et al.

Preprint: Cryo-EM structure of the Type IV pilus extension ATPase from enteropathogenic Escherichia coli – Ashok R. Nayak, et al.

Preprint: Accumulation of defense systems drives panphage resistance in Pseudomonas aeruginosa – Ana Rita Costa, et al.

Preprint: Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility can lead to increased zoliflodacin resistance – Daniel H. F. Rubin, Tatum D. Mortimer, and Yonatan H. Grad

Preprint: A contractile injection system mediates developmentally regulated intra-strain cell death in Streptomyces coelicolor – Maria Vladimirov, et al.

Gut microbiome

Vertical transmission of the gut microbiota influences glucose metabolism in offspring of mice with hyperglycaemia in pregnancy – Cunxi Xue, et al. Microbiome

Phages and viruses

Preprint: Genetic differences between 129S substrains affect antiretroviral immune responses – Robert Z. Zhang, et al.

Preprint: The dissemination of Rift Valley fever virus to the eye and sensory neurons of zebrafish larvae is stat1 dependent – S. ter Horst, et al.

Preprint: HIV-1 latent infection triggers broader epigenomic and transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells – Gabrielle Lê-Bury, et al.

Preprint: Pelagibacter phage Skadi – An abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth – Holger H Buchholz, et al.

Preprint: A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency – Bingyu Yan, et al.

Preprint: Identification of β2 microglobulin, the product of B2M gene, as a Host Factor for Vaccinia Virus Infection by Genome-Wide CRISPR genetic screens – Alejandro Matía, et al.

Preprint: Generation of Recombinant Rotaviruses Expressing Human Norovirus Capsid Proteins – Asha A. Philip and John T. Patton

Preprit: Distantly related hepaciviruses share common entry factor, Claudin-1 – Kamilla Toon, et al.

Preprint: Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry – Samantha Hover, et al.

General microbiome

Preprint: Effects of Cr stress on bacterial community structure and diversity in rhizosphere soils of Iris pseudacorus – Zhao Wei, et al.

Preprint: Lack of specificity in Geobacter periplasmic electron transfer – Sol Choi, Chi Ho Chan, and Daniel R. Bond

Preprint: Lipidomic analysis reveals differences in Bacteroides species driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids – Eileen Ryan, et al.

Preprint: Turnover of the extracellular polymeric matrix in an EBPR microbial community – Sergio Tomás-Martínez, et al.

Preprint: An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State – Griffin Chure and Jonas Cremer

Preprint: Cryo-ET of infected cells reveals that a succession of two lattices drives vaccinia virus assembly – Miguel Hernandez-Gonzalez, et al.

Preprint: Soil protists can actively redistribute beneficial bacteria along Medicago truncatula roots – Christopher J. Hawxhurst, et al.

Developing whole cell standards for the microbiome field – Chrysi Sergaki, et al. Microbiome


Preprint: The capacity to configure the hymenophore is not confined to the pore field in Oak mazegill (Daedalea quercina, Polyporales) – Bjarke Jensen

Preprint: Epigenetic Changes in Saccharomyces cerevisiae Alters the Aromatic Profile in Alcoholic Fermentation – Yanzhuo Kong, et al.

August 1st, 2022

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.


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


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.

July 18th, 2020

God morgon! Good morning from Sweden. Today’s digest features only three articles but I am sure everyone will enjoy reading it, especially a super interesting article highlighting the importance of older siblings on development of an individual’s airway and gut microbiota. The study asserts that having a closely aged older sibling has more impact on one’s microbiota as compared to having more than one older sibling. Another featured article demonstrates how gut microbiota can improve the quality of chicken by preventing intestinal inflammation. From animal farming we go over to plant farming. Another article in today’s digest shows how monocropping (growing the same crop over and over) negatively impacts the diversity of soil bacteria which eventually shows up as poor yield. This makes it imperative to consider the soil microbiota while taking decisions on crop cycle. I hope you will enjoy reading today’s digest and have a great week!

Human microbiome

The developing airway and gut microbiota in early life is influenced by age of older siblings – Emil Dalgaard Christensen, et al., Microbiome

Animal microbiome

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang, et al., Microbiome

Plant root and soil microbiome

Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems – Pengfa Li, et al., Microbiome

March 29th, 2021

God morgon!

Good morning from Sweden. I know everyone is looking forward to a long weekend, but today is just Monday.

Today’s digest begins with a new visualisation tool for microbiome analysis in R – animalcules. In another study, probiotic yeast metabolites were reported to inhibit bacterial virulence. It is yet another evidence in support of the fermented milk-based probiotic drinks. Talking about the diet, a team of researchers has found the commonly used dietary emulsifiers have a detrimental impact on the gut microbiome. A new study on studying the microbiome using PCR amplification and sequencing illustrates how off-target amplification can introduce a lot of problems. The study in question compared the brain microbiome of healthy individuals and individuals with Parkinson’s disease. Another study has shown how reduced genome provides certain bacteria an advantage in thriving during coastal dinoflagellate blooms.

Elsewhere in the digest are preprints describing a new broad spectrum antifungal, Kenyan traditional medicine as an approach to tackle antibiotic resistance, and prediction of antibiotic resistance using machine learning approach.

Hope you like today’s collection!

Computational Biology

animalcules: interactive microbiome analytics and visualization in R – Yue Zhao, et al., Microbiome

Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Alberto Pascual-García, Microbiome

Preprint: Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes– Sam Benkwitz-Bedford, et al.

Environmental Microbiome

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms – Yu Han, et al., Microbiome

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals– T. Keller-Costa, et al., Microbiome

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques – Mareike C. Janiak, et al., Microbiome

Holo-omics for deciphering plant-microbiome interactions – Ling Xu, et al., Microbiome

General Microbiome

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals – Janis R. Bedarf, et al., Microbiome

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome – Julien Tap, et al., Microbiome

Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites – Orit Malka, et al., Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics – Yuan Lin, et al., Microbiome

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Sabrine Naimi, et al., Microbiome

Preprint: Paenibacillus sp. strain UY79, isolated from a root nodule of Arachis villosa, displays a broad spectrum of antifungal activity – Andrés Costa, et al.

Bacteria Hysteria

Preprint: Accessory genomic epidemiology of co-circulating Acinetobacter baumannii clones – Valeria Mateo-Estrada, et al.

Preprint: Kenyan Traditional Medicine: Exploring Old Solutions to the Modern Antibacterial Crises Through Natural Products Chemistry – Fidensio K. Ndegwa, et al.

Preprint: The Detection of Bergeyella zoohelcum in Young Children after Cat Bite – Min Hu, et al.

Preprint: Chromatic bacteria version 2 – A Himar1 transposon based delivery vector to extend the host range of a toolbox to fluorescently tag bacteria – Christian F Stocks, et al.


Preprint: Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling – Taylor L. Light, et al.

Preprint: Th17 cell master transcription factor RORC2 regulates HIV-1 gene expression and viral outgrowth – Tomas Raul Wiche Salinas, et al.

Preprint: Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses – Fatima Aysha Hussain, et al.

March 15th, 2021

God morgon!

Good morning from Sweden. Another Monday, a new week, and a new digest.

Today’s digest comes with a new review on gut microbiota focusing on the mycobiota which is mostly overlooked as a bulk of studies focus their interest on bacterial diversity in the gut instead. A very cool feature, which I think is now fast becoming common in papers published in Microbiome is the use of a very informative video abstract. As I mentioned in my previous digest, a video abstract catches the eye and it could very well be the next big thing in academic publishing.

There is some potential bad news from Brazil as a team has identified a new nCoV variant of interest (VoI) which probably originated in August 2020 and accounted for about 3% of all samples analyzed between November 2020 and February 2021. The variant also accounted for a very high fraction (35%) of all the B.1.1.33 lineage samples analyzed during the aforementioned period and is now considered widely distributed in Brazil. The troubling fact is that this variant has a S:E484K mutation in the spike protein and this mutation has been implicated in immune evasion and resistance to several monoclonal antibodies. Speaking about COVID-19, there is a new study that tested the viability of nCoV on various inanimate surfaces. The virus persisted longest on a surgical mask (for about 124 hours) and reduced the fastest on a polyester shirt (about 2.5 hours).

Elsewhere in the digest is a preprint that analysed publically available datasets to determine the effect of space type radiation on the gut microbiome, a somewhat controversial study (check out the comments section) hypothesizing the use of fungus to attenuate ionizing radiation on the ISS, and a comprehensive study of E. coli phage-host interactions within the BASEL phage collection.

Hope you’ll enjoy today’s digest.

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities – Xiaoyan Wu, et al., Microbiome

Preprint: A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil – Paola C Resende, et al.

Preprint: Persistence of SARS-CoV-2 virus and viral RNA on hydrophobic and hydrophilic surfaces and investigating contamination concentration – Susan Elizabeth Paton, et al.

Preprint: Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection – Enea Maffei, et al.

Preprint: PulseNet international: the missing link between PFGE and WGS – Ibrahim El-khalil M Adam

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

Preprint: A Self-Replicating Radiation-Shield for Human Deep-Space Exploration: Radiotrophic Fungi can Attenuate Ionizing Radiation aboard the International Space Station – Graham K. Shunk, Xavier R. Gomez, and Nils J. H. Averesch

Preprint: Resistance to aztreonam in combination with non-β-lactam β-lactamase inhibitors due to the layering of mechanisms in Escherichia coli identified following mixed culture selection – Ching Hei Phoebe Cheung, et al.

Preprint: Yersinia pestis lipopolysaccharide remodeling confers resistance to a Xenopsylla cheopis cecropin – Basil Mathew, Kari L. Aoyagi, and Mark A. Fisher

Preprint: Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults – Benjamin A Siranosian, et al.

Preprint: Radiation Threats to Humans in Space and an alternative approach with Probiotics – Dilara Diken, et al.

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.


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.


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.


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.


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.


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


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!


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


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


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


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.


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!


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.


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


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.


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