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

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

I hope everyone is staying safe and healthy during this pandemic. Today’s digest will start with a few articles on COVID-19 before moving on to microbiome papers.

COVID-19

Preprint: A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing – Itokawa et al.

Preprint: FDA approved drugs with broad anti-coronaviral activity inhibit SARS-CoV-2 in vitro – Weston et al.

Protein Structure and its Sequence Reanalysis of 2019-nCov Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1 – Zhang et al. – ACS Publications

General Microbiome

Antithetic population response to antibiotics in a polybacterial community – Laporta & Ojalvo – ScienceAdvances

Review: Toward a dynamical understanding of microbial communities – Rainey & Quistad – Royal Society Publishing

Pregnancy and early life

Beyond the Bacterial Microbiome: Virome of Human Milk and Effects on the Developing Infant – Mohandas & Pannaraj – Karger

Human vaginal microbiome

Cervicovaginal microbiome and natural history of HPV in a longitudinal study – Usyk et al. – PLOS Pathogens

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta et al. – Springer Link

Human gut microbiome

Review: Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature – Frame & Jackson – Nutrition Reviews

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long et al. – Nature

The effects of daily fasting hours on shaping gut microbiota in mice – Li et al. – BMC Microbiology

Human oral microbiome

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Effects of Chlorhexidine mouthwash on the oral microbiome – Bescos et al. – Scientific Reports

Animal microbiome

Microbiome diversity and composition varies across body areas in a freshwater turtle – McKnight et al. – Microbiology Society

Gut microbiota shifts in the giant tiger shrimp, Penaeus monodon, during the postlarvae, juvenile, and adult stages – Cicala et al. – Springer Link

Plant and soil microbiome

Community-driven Metadata Standards for Agricultural Microbiome Research – Dundore-Arias et al. – APS Publications

Do cover crops benefit soil microbiome? A meta-analysis of current research – Kim et al. – ScienceDirect

Water and extremophile microbiome

Linking regional shifts in microbial genome adaptation with surface ocean biochemistry – Garcia et al. – The Royal Society Publishing

The potential impact of bacterial communities exposed to crude oil and light on the growth of the harmful algal blooming species Karenia brevis (Dinophyceae) – Park & Buskey – CSIRO Publishing

Preprints

Machine-learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection – Ciucci et al.

Infrared absorptions as indicators for Pseudomonas aeruginosa and Acinetobacter baumannii – Yamamoto et al.

Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments – Lloyd et al.

A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms – Long et al.

Lecturer at University College Dublin, Ireland, in the School of Biomolecular and Biomedical Sciences. I teach Image Science, 3D imaging and Model systems. I have 15 years experience in imaging from microscope design to image analysis with a BIG favorite: Light Sheet Microscopy. I also like to do underwater imaging and Environmental Imaging.