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)

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.