April 08, 2020

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Good morning. This is my first contribution to the Microbiome Digest. It is an interesting opportunity to survey some of the current literature and areas of research, and I hope that the literature summarized below will be of interest to readers. Today’s digest also includes articles on covid-19. There are two publications on metabolomic and/or proteomic profiling of covid-19 patients, and one which analyzes genetic variants of the ACE-2 protein across a database taken from the Italian population. A topic of personal interest to me is how and whether the level of glycosylation and sialylation on the ACE-2 protein and on the coronavirus spike protein may influence binding and covid-19 infectivity. However, this is not covered in the publication.

The two papers in the pregnancy and early life section discuss the development of the infant microbiome, with regard to dysbiosis in preterm infants and with regard to the contribution of maternal milk-derived microbes.

The extremophile paper by Roy et al. looks at the microbial population in boron-rich extremophile environments. Alkyl borates are known to form boronate complexes with saccharides and it would be interesting to profile the enzymatic functions of these strains for potential borate-metabolizing capability.

The techniques paper by Fergusson et al. describes the building of a mass spectral database by which Burkholderia and related bacterial strains can be identified from their MALDI-TOF metabolite profile, using the Bruker Biotyper platform. Both nucleic acid sequencing and metaproteomic tools were invoked by An et al., in their Ecotoxicology paper investigating the mechanism of microbial metabolism of toxic dye molecules in the environment.

Several papers discuss correlations between microbial populations and disease states. For example, Tengeler’s paper describes the use of MRI to to study the effects on the brains of germ-free mouse brains, following transplantation of gut bacteria from humans with and without ADHD, while Zheng et al. describe microbiome signatures which correlate with lung cancer.

Under the Market Analysis section, a $38M deal between Second Genome and Gilead has been announced.

Covid-19
Preprint:
The relationship of COVID-19 severity with cardiovascular disease and its traditional risk factors: A systematic review and meta-analysis
Matsushita, K. et al.

Preprint:
Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking
Mahapatra, S. et al.

Preprint:
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Bo Shen et al.

Preprint:
Plasma Metabolomic and Lipidomic Alterations Associated with COVID-19
Wu, D. et al.

Preprint:
Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
Wikramaratna, P. et al.

Preprint:
ACE2 variants underlie interindividual variability and susceptibility to COVID-19 in Italian population
Renieri, A. et al.

General Microbiome

MP10-18 FUNCTIONAL ANALYSIS OF THE URINARY TRACT MICROBIOME OF CALCIUM OXALATE STONE FORMERS
N Kachroo et al,
The Journal of Urology, 2020

Microbial Engineering Community (mce): Selecting Key Players in Microbiomes
CEG Camacho et al.
Chemical Engineering Transactions, 2020

Pregnancy and early life

Contributors to Dysbiosis in Very-Low-Birth-Weight Infants
MW Groer et al.
Journal of Obstetric, Gynecologic, & Neonatal Nursing, 2020

A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women
CA Stennett et al.
PLOS one, 2020

Milk Microbiome and Neonatal Colonization: Overview.
S Rautava
Nestle Nutrition Institute workshop series, 2020

Oral Microbiome

Single-Cell Genomics and the Oral Microbiome
M Podar et al.
Journal of Dental Research, 2020

Dysbiosis of saliva microbiome in patients with oral lichen planus
Fei Yan Yu et al. BMC Microbiology, 2020

Gut Microbiome

Specific gut microbiome signature predicts the early-stage lung cancer
Yajuan Zheng et al.
Gut Microbes, 2020

Complex influences of gut microbiome metabolism on various drug responses
Sihyun Chae et al.
Translational and Clinical Pharmacology, 2020

Gut Microbiota, Its Role in Induction of Alzheimer’s Disease Pathology, and Possible Therapeutic Interventions: Special Focus on Anthocyanins
MS Khan et al.
Cells, 2020

Faecal microbiota transplantation: indications, evidence and safety
WT Soo et al.
Australian Prescriber, 2020

PhD Thesis:
The effect of faecal microbiota transplantation in irritable bowel syndrome. A double blind, randomized placebo controlled single centre study
Peter Johnsen

Animal Experiments
Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice
Anouk C. Tengeler et al.
Microbiome 2020

Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents
Xifan Wang et al.
Gut, 2020

Animal Microbiome
The microbiota of dairy milk: a review
Eugenio Parente
International Dairy Journal, 2020

Plant, root and soil Microbiome
Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu
T Liu et al.
FEMS Microbiology Ecology, 2020

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting
WJ Emsens et al.
The ISME Journal, 2020

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis.
J Chen et al.
Microbial biotechnology, 2020

Insights into the earthworm gut multi-kingdom microbial communities
R Sapkota et al.
Science of the Total Environment, 2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil
MJ Zwetsloot et al.
Soil Biology and Biochemistry, 2020

Extremophile Microbiomes
Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica
EM Bottos et al.
FEMS Microbiology Ecology, 2020

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics
Weipeng Zhang et al.
Microbiome 2020

Integrated metagenomic and metaproteomic analyses reveal potential degradation mechanism of azo dye-Direct Black G by thermophilic microflora
X An et al.
Ecotoxicology and Environmental Safety, 2020

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau
C Roy et al.
Scientific Reports, 2020

Microbes in Built Environments

An in-depth survey of the microbial landscape of the walls of a neonatal operating room
D Derilus et al.
PLOS ONE, 2020

Phages and Viruses

Preprint:
Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe
DE Campbell et al.

Bioinformatics and Techniques

Development of a Custom MALDI-TOF Mass Spectrometric Database for Identification of Environmental Burkholderia and Related Genera.
CH Fergusson et al.
Environmental Microbiology, 2020

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
Eli Levy Karin et al.
Microbiome 2020

Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories
Shan Sun et al.
Microbiome 2020

Preprint:
DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform
Sophie George et al.

Preprint:
Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Noam Auslander et al.

Multiview learning for understanding functional multiomics
ND Nguyen et al.
PLOS Computational Biology, 2020

Microbes on the Market

News Article:
Gilead agrees microbiome deal with Second Genome
Ben Hargreaves, Biopharma Reporter

Market Report:
Human Microbiome Market Future Outlook 2020-2026. Major Players are Dohme Corp, Seres …
Science In Me

Market Report:
Europe Human Microbiome Market to Offer Increased Growth Prospects for Manufacturers up to 2025
Sameer Joshi, Curious Desk (blog)



April 7, 2020

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Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!

COVID-19

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

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

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al. – Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiome – EurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com

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!

April 5, 2020.

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All the break-neck speed with which the progress that is happening today in tracking, detecting and treating the disease, like everything else, is owed in part to the giants whose shoulders we’re standing on. One such thing is the usage of serum (from recovered patients or derived elsewhere) for treatment. So, as a little tribute, I would like to share with you today, on the birthday of Dr. Hattie Elizabeth Alexander (born April 5, 1901), the information that she pioneered the work in using anti-influenzal rabbit serums to treat the then always-fatal influenzal meningitis (effectively bringing down the fatality rate to 20%!), and was also sone of the very first to study bacterial mutations that come along with antibiotic resistance !

So we’ve come a long way and are forging our way forward. Here are a few interesting articles that are slowly pushing this boundary, a piece at a time.

COVID-19

From PREDICT to prevention, one pandemic later – Colin J Carlson – The Lancet.

Human Microbiome

Review: Risk factors associated with gastric malignancy during chronic Helicobacter pylori infection – Ami Y Seegar – Medical Research Archives.

Review: From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism – Ara Koh – Molecular Cell.

Pregnancy and Early Life

Breast Milk and Microbiota in the Premature Gut: A Method of Preventing Necrotizing Enterocolitis – Orga PL et al – Karger.

Human Brain and Microbiome

Book: Integrative and Functional Medical Nutrition Therapy. Chapter: The Microbiome and Brain Health – Sharon L. Norling -Springer

Animal Experiments


Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). Wanping Aw et al – NPJ Science of Food.

Botany

Rhizobacteriome: Promising Candidate for Conferring Drought Tolerance in Crops – Vinod Yadav et al – Journal of Pure Applied Microbiology

Legionella species: A potential problem associated with rain water harvesting systems? – Judith A Taylor et al – SAGE Journals

Bioinformatics

Applications of Machine Learning Predictive Models in the Chronic Disease Diagnosis – Gopi Battineni et al – Journal of Personalized Medicine

PS: I know, I am with you on this — the lockdown isn’t ideal. But we are also the generation, who for the first time can end articles signing off as “Stay Safe and Wash Your Hands” and manage to prevent a large proportion of its species from suffering / dying. Isn’t that crazy! Have a great day!

More information on Dr. Hattie Elizabeth Alexander — here and here.

April 4, 2020

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Good morning and salutations from Singapore! This is the first digest that I’m contributing for the blog, so I hope my selections are interesting to you all! Today’s digest begins with some recent COVID-19 pre-prints, before getting into papers on a diverse range of microbiome-related topics. Highlights today include a study on cats potentially harbouring SARS-CoV-2 (nooo…), the effect of C-section birth on the vaginal microbiota of adult women, and the impact of the virome on biogeochemical cycling in Lake Baikal.

COVID-19

Preprint: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia – Pizzorno et al.

* Preprint: SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation – Zhang et al.

Preprint: Direct RNA sequencing and early evolution of SARS-CoV-2 – Taiaroa et al.

General microbiome

Review: Microbiota and metabolites in rheumatic diseases – Tong et al. – Autoimmunity Reviews

Human respiratory microbiome

Preprint: Distinctive airway microbial ecology of smokers and asthmatics – Turek et al.

Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort – Bouquet et al. – Respiratory Research

Human gut microbiome

An in vitro evaluation of the effects of different statins on the structure and function of human gut bacterial community – Zhao et al. – PLoS ONE

Human vaginal microbiome

* A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women – Stennett et al. – PLoS ONE

Animal experiments

Polysaccharide extracted from WuGuChong reduces high-fat diet-induced obesity in mice by regulating the composition of intestinal microbiota – Wang et al. – Nutrition & Metabolism

Animal microbiome

Intestinal microbes: an axis of functional diversity among large marine consumers – Scott et al. – Proceedings of the Royal Society B

Plant, root, and soil microbiome

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: Accelerated biodegradation or toxicity? – Katsoula et al. – FEMS Microbiology Ecology

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species – Yao et al. – Applied Soil Ecology

Water and extremophile microbiome

* Preprint: New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal – Coutinho et al.

Bioinformatics

Ten simple rules for providing effective bioinformatics research support – Kumuthini et al. – PLoS Computational Biology

Finally, remember that physical isolation doesn’t have to mean social isolation. Call someone you haven’t talked to in a while, I’m sure they’ll appreciate it! You’re doing great 😀

April 3, 2020

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Good morning from the UK. This is my first post for Microbiome Digest, so I hope that my ‘picks’ are interesting and suitable. I have included one link which I hope will make you smile – see if you can spot it 😀 I’m on day 22 of my social isolation with the potential of many more months to come. I’ve been looking forward to doing this as I am unable to do much work as a result of this pandemic; something that most of us are suffering from, unless you are working on the latest novel Coronavirus. I  know at least one person whose workload has escalated dramatically.  It’s certainly an interesting and challenging time for microbiologists!

Covid-19

Unveiling the origin and transmission of 2019-nCov (Cell.com: Trends in Microbiology)

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade (Science Direct: Antiviral Research)

CD-sACE2 Inclusion Compounds: An Effective Treatment for Corona Virus Disease 2019 (COVID-19) (Wiley Online Library: Preprint)

General microbiome

When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii† (Wiley Online Library: Cellular Microbiology)

Human gut microbiome

Horizontal transfer of antibiotic resistance genes in the human gut microbiome (Science Direct: Current Opinion in Microbiology)

Gut microbiome composition and diversity-related to human personality traits  (Science Direct: Human Microbiome Journal)

Animal microbiome

Rapid multi-residue screening of antibiotics in muscle from different animal species by microbiological inhibition method (Science Direct: Microchemical Journal)

Phages and viruses

Binding of pDNA with cDNA using hybridization strategy towards monitoring of Haemophilus influenza genome in human plasma samples (Science Direct: International Journal of Biological Macromolecules)

Plant, root and soil microbiome

Unravelling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot (Wiley online library: Environmental Microbiology)

Techniques

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture(Nature.com: Scientific Reports)

Identification and quantification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes for aquatic microbiological risk assessment (Science Direct: Water Research)

I hope that you have found at least one interesting paper to read. Should you be in ‘lockdown’ it beats binging on Netflix or staring at the four walls! If you’re writing up your thesis – well, everyone needs a break 😉

Karen

April 2, 2020

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Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

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

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Yu et al. – PLOS Medicine

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports

Probiotics

Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports

April 1, 2020

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Hello Everyone, I am excited for my first post here. Continuing the trend the first few papers are on COVID-19 : first one talks about its classification and nomenclature. I hope everyone is staying safe and healthy. Last but not the least, keep up the hand washing.

COVID-19

* The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2- Coronaviridae Study – Group of the International Committee on Taxonomy of Viruses – Nature Microbiology

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses – Letko et al. – Nature Microbiology

General microbiome
Variation in prostaglandin metabolism during growth of the diatom Thalassiosira rotula – Dato et al. – Scientific Reports

Pregnancy and early life
Factors affecting early-life intestinal microbiota development – Vandenplas et al. – Nutrition

Multi-site human microbiome
Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age – Chaudhari et al. – Scientific Reports

Human gut microbiome
Implication of the gut microbiome composition of type 2 diabetic patients from northern China – Li et al. – Scientific Reports

The microbiota programs DNA methylation to control intestinal homeostasis and inflammation– Ansari et al. – Nature Microbiology

Animal microbiome
The Contest of Microbial Pigeon Neighbors: Interspecies Competition Between Serratia marcescens and the Human Pathogen Cryptococcus neoformans – Haleva et al. – Fungal Biology

Plant, root, and soil microbiome
Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth – Chu et al. – Microorganisms

Phages and viruses
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains – Requião et al. – Scientific Reports

*Review: 5 challenges in understanding the role of the virome in health and disease – Wang David – PLOS Pathogens

Bioinformatics
Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment – Rachlin et al. – Scientific Reports

Techniques
Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture – Cummings et al. – Scientific Reports

Review: Potential of proteomics to probe microbes – Matilda et al. – Journal of Basic Microbiology

March 31st, 2020

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Hello all, this is my first post on the blog. Following earlier trends, I will begin with news on COVID-19. Stay safe, everyone.

COVID – 19

Preprint: Ocular conjunctival inoculation of SARS-CoV-2 can cause mild COVID-19 in Rhesus macaques – Deng. et al

Preprint: Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution – Kumar et al. 

Human Gut Microbiome

Gut Microbial Metabolites Induce Changes in Circadian Oscillation of Clock Gene Expression in the Mouse Embryonic Fibroblasts – Ku et al. – Molecules and Cells

Plant, Root, and Soil Microbiome

Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy – Aiello et al. – MycoKeys

Food Microbiology

The impact of hybrid yeasts on the aroma profile of cool climate Riesling wines – Kanter et al. – Food Chemistry: X

Phages and Viruses

Preprint: A novel antiviral formulation inhibits a range of enveloped viruses – Fletcher et al. 

March 30, 2020

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Please stay home and help flatten the curve! Continuing the past few days, the first papers will be COVID-19 related

COVID-19
Preprint: SARS-CoV-2 specific antibody responses in COVID-19 patients Okba et al.

Anti–spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection Liu et al.

Human Vaginal Microbiome
Study Protocol: Protocol for a Longitudinal Analysis of the Vaginal Microbiome from a Pregnant Cohort of African Women in Nigeria Odogwu et al.

Human Gut Microbiome
Ruminococcus gnavus bacteremia, an uncommon presentation of a common member of the human gut microbiota: case report and literature review Lefever et al.

Water Microbiome
Preprint: Dissecting the toxicity and mitigating the impact of harmful Prymnesium blooms in the UK waters of the Norfolk Broads Wagstaff et al.

Techniques
Preprint: Internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples Janes et al.

Microbes in the News
Study explores the beneficial effects of healthy dietary patterns on gut microbiome mental_daily