May 21, 2020

There is a wide range of interesting articles and topics in today’s digest.
For example, an article by McGenity et al. discusses education, and how to communicate the importance of microbes and the microbiome to the general population. There is a discussion by Xi et al. on how specific oligosaccharide molecules such as stachyose (found in human milk and various vegetables) can modulate the intestinal microbiota and thereby influence the immune system in early life, and a discussion on how the iminosugar drug Miglustat might be repurposed as a Covid-19 therapy. Gradilla-Hernandez et al discuss the use of a simulated gut system to model the interactions and relative growth of gut microbial strains under different conditions, using differential neural network approaches.
I find it fascinating to think of the gut microbiome as an ecological system, and the papers on tryptophan and on the interactions between rotavirus and gut bacteria, mediated by host glycans, speak to this.
Development of any microbiome-based therapeutics will need to consider formulation, delivery, and release/engraftment of the product, and the paper by Chang et al. discusses the development of oral formulations for Akkermansia muciniphila.
One significant mechanism by which the microbiome affects human health is via the products of bacterial metabolism. Johnson et al. discuss how the production of sphingolipids by gut bacteria can affect host sphingolipid and ceramide levels and utilization, and the review by Weersma et al. discusses the field of “pharmacomicrobiomics”, whereby bacterial metabolism can influence the fate of drugs doses to patients, increasing the magnitude of differences in patient-to-patient response. The microbiome has also been implicated in many chronic human health conditions, and the paper by Matenchuk et al. discusses the influence of gut bacteria on circadian rhythms and sleep patterns. Finally, Burberry et al. discuss the interplay between anti-inflammatory gut bacteria and the effects of the C9orf72 mutation which contributes to ALS/Lou Gehrig’s disease and frontotemporal dementia.

General Microbiome
Tryptophan as a Central Hub for Host/Microbial Symbiosis
M Borghi et al.
International Journal of Tryptophan Research, 2020

Host–microbiome interactions: the aryl hydrocarbon receptor as a critical node in tryptophan metabolites to brain signaling
N Ma et al.
Gut Microbes, 2020

Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes
TJ McGenity at al.
Microbial Biotechnology, 2020

Pregnancy and early life
Stachyose increases intestinal barrier through Akkermansia muciniphila and reduces gut inflammation in germ-free mice after human fecal transplantation
M Xi et al.
Food Research International, 2020

Extremophile Microbiomes
Preprint:
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys
J Hou et al.

Covid-19
Preprint:
Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.
JB Case et al.

Preprint:
Repurposing of Miglustat to inhibit the coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2
S Rajasekharan et al.

Animal Microbiome
Preprint:
Effects of parity, blood progesterone, and non-steroidal anti-inflammatory treatment on the dynamics of the uterine microbiota of healthy postpartum dairy cows
OB Pascottini et al.

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance
M-Y Xue et al.
Microbiome 2020

Techniques
Applying Differential Neural Networks to Characterize Microbial Interactions in an Ex Vivo Gastrointestinal Gut Simulator
MS Gradilla-Hernández et al. 
Processes, 2020

Oral Microbiome
Longitudinal Study of Oral Microbiome Variation in Twins
M Freire et al.

Scientific Reports, 2020

Antimicrobial peptide GH12 prevents dental caries by regulating dental plaque microbiota
W Jiang et al.
Applied and Environmental Microbiology 2020

Microbes in built environments
Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters
J Hüpeden et al.
Aquacultural Engineering, 2020

Human vaginal microbiome
Preprint: Structure and regulation of the cervicovaginal microbiome in a cohort of Afro-Caribbean women
O Roachford et al.
Microbiome, 2020

Phages and Viruses
Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence
M Engevik et al.,
Gut Microbes, 2020

Pharmacological interventions
Preprint:
The Changes of Gut Microbiota in Drug-Naïve First-Episode MDD Patients Under Treatment by SSRIs
Y Shen et al.
BMC Psychiatry 2020

Interaction between drugs and the gut microbiome
RK Weersma at al.

Gut, 2020

The Therapeutic Optimization of the Gut Microbiota in Diabetes Management
P Davidson et al.
ADCES in Practice, 2020

Improved viability of Akkermansia muciniphila by encapsulation in spray dried succinate-grafted alginate doped with epigallocatechin-3-gallate
Y Chang et al.

Gut Microbiome
The probiotic L. casei LC-XCAL™ improves metabolic health in a diet-induced obesity mouse model without altering the microbiome
CJ Walsh et al.
Gut Microbes, 2020

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota
S Namasivayam et al.
PLOS Neglected Tropical Diseases, 2020

Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels
E Johnson et al.,
Nature Communications 2020

Sleep, Circadian Rhythm, and Gut Microbiota
BA Matenchuk et al.
Sleep Medicine Reviews, 2020

C9orf72 suppresses systemic and neural inflammation induced by gut bacteria
A Burberry et al.
Nature, 2020

Market Analyses
Market Report:
Human Microbiome Market Insights & Deep Analysis, Future Scenario Till 2025 | Enterome …
News Distinct

Market Report:
COVID-19 Impact on Human Microbiome Sequencing Technology Market Research Report …
3rd Watch News

Market Report:
Pre, pro- and microbiotics and your business
Natural Products INSIDER

Market Report:
Microbiome Sequencing Services Market Types, Applications And Competitors 2019-2025 …
openPR (press release)

Market Report:
PGR decision provides much-needed clarity in fast-growing microbiome space
IAM (blog)

Market Report:
Human Microbiome Market Research Report 2020 By Size, Share, Trends, Analysis and Forecast …
Cole of Duty

Market Report:
Human Microbiome Market size, historical growth, analysis, opportunities and forecast to 2026 …
Surfacing Magazine

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.

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)