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:
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