April 08, 2020

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.

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

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

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

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

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

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

General Microbiome

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

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

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

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)

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