April 3, 2020

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!


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)


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 😉


April 2, 2020

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


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

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.


* 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 РRequịo et al. РScientific Reports

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

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

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

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

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

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.

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

Longing for the lab

I’m a final year PhD student, studying the relationship between gut bacteria and colon cancer using a benign cell line model. Last Tuesday, the UK government announced a lockdown, and those institutions that were still open, closed their doors.

So, like a batch of fresh samples, my experiments have been put on ice. It’s a scary time for a lot of fledgling researchers, with no contingency plan for bursary or lab time extensions currently in place. Many PhD students, like myself, will find themselves attempting to write thesis chapters a lot earlier than they had planned.

I’ve witnessed first hand, as my peers have battled through the ordeal, that tackling the big beast of thesis writing can lead to all kinds of delirium. In my recent writing-induced malaise, I’ve found myself longing to be back in lab. Surprisingly, I’m even finding myself reminiscing about some of the more tedious tasks, such as:

  1. Passaging cell lines. Looking after cells, particular benign or primary cell lines, is like having a child. They always need something, and if you dare to upset them, pray for your lab results/sanity. Shared tissue culture facilities also pose their own problems, and I’m sure most cell biologists would admit to a small level of constant paranoia: Are my cells ok? But, what I wouldn’t give for the simplicity of easing myself into a busy week of lab work by splitting a flask of cells on a Monday morning.
  2. Visiting the liquid nitrogen freezer. Liquid nitrogen freezers are scary. Lab managers just love to regale fresh inductees with horror stories as a way of teaching the importance of appropriate eye protection. They’re also usually kept somewhere out of the way and with good ventilation. In my experience, this is almost exclusively a damp, cold, cellar-like room somewhere far, far away from where you actually conduct your lab work. There is, however, a sort of tranquility about lifting the lid off of the freezer, and watching the gas silently flow out like the world’s quietest volcano.
  3. Transporting samples between labs. As part of my work, I’m lucky enough to work with some foul-smelling anaerobic bacteria. Fortunately, the university moved on from anaerobic jars long before I started, and we have a rather high-end anaerobic workstation. The problem, however, is that this workstation is not in the main microbiology lab, but a smaller lab approximately 3 feet down the corridor. We have no open lab zone, so this means painstakingly sealing, bagging and boxing all cultures, in order to, for example, read them on a spectrophotometer that’s a mere 20 paces away. Come to think of it, maybe I don’t miss this so much.

Perhaps the biggest challenge many of us are facing right now is that of isolation. The hustle and bustle of a busy lab is gone, supervisors are more distant, and there are no fellow researchers to complain to about a failed experiment (or a cantankerous lab manager). Hopefully by facilitating discussion and keeping connected, we can make getting through this difficult time a little easier.

What are you missing about science? Comment below!

March 29, 2020

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.


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


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.