Human microbiome

The interplay between immune system and microbiota in gynecological diseases: a narrative review – Villa et al. – European Review for Medical and Pharmacological Sciences

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians –  Rubel et al. – Genome Biology

Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets – Xu et al. – Gut Microbes

Dissimilarity of Airway and Lung Tissue Microbiota in Smokers undergoing Surgery for Lung Cancer – Reinhold et al. – Microorganisms

Chemotherapy-induced ileal crypt apoptosis and the ileal microbiome shape immunosurveillance and prognosis of proximal colon cancer – Roberti et al. – Nature Medicine

Animal microbiome

Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus) – Yang et al. – PeerJ

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic E. coli F18 – Li et al. – Frontiers in Microbiology

The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics – Nettles et al. – Microbial Ecology

Food microbiome

Assessment of overall microbial community shift during Cheddar cheese production from raw milk to aging – Choi et al. – Applied Microbiology and Biotechnology

Marine microbiome

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan – Sichert et al. – Nature Microbiology

Scientific communication and education

Preprint: A rapid urban biodiversity blitz using aquatic environmental DNA – Hupalo et al. – bioRxiv

Preprint: The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic – Fox – bioRxiv

Greetings from Colorado. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications including the human tumor microbiome by Nejman et al., microbial colonization in the neonatal gut microbiome by Wang and Dominguez-Bello, and drought effects on the millet root microbiome together with many more interesting papers. Enjoy.

COVID-19

Antimicrobial resistance in the age of COVID-19 – Editorial – Nature Microbiology

Metatranscriptomic Characterization of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling – Zhang et al. – Clinical Infetious Diseases

General microbiome

Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Beck et al. – bioRxiv

Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes– Kazemian et al. – bioRxiv

Human microbiome

The human tumor microbiome is composed of tumor type–specific intracellular bacteria – Nejman et al. – Science*

Animal experiments

Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats – Bosco-Lauth et al. – bioRxiv

The heart microbiome of insectivorous bats from Central and South Eastern Europe – Corduneanu et al. – bioRxiv

Gut microbiome

Microbial colonization alters neonatal gut metabolome – Wang and Dominguez-Bello – Nature Microbiology

Plant, root, and soil microbiome

Breeding for resistance: can we increase crop resistance to pathogens without compromising the ability to accommodate beneficial microbes? – Zuccaro and Langen – New Phytologist

Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses – Jean et al. – New Phytologist

Drought Drives Spatial Variation in the Millet Root Microbiome – Simmons et al. – Frontiers in Plan Science*

Streptomyces’ scent attracts spore dispersers – Rohlfs – Nature Microbiology*

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al. – bioRxiv

Good Friday, everyone. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications. Have a nice weekend.

COVID-19

Treatments in the COVID-19 pandemic: an update on clinical trials – Tao – Expert Opinion on Emerging Drug

Ozone Treatment for Elimination of Bacteria and SARS-CoV2 for Medical Environments – Westover et al. – bioRxiv

Coronavirus, as a source of pandemic pathogens – Konishi – bioRxiv

Nature news

Are women publishing less during the pandemic? Here’s what the data say

Coronavirus vaccine trials have delivered their first results — but their promise is still unclear

How to address the coronavirus’s outsized toll on people of colour

Human Microbiome

The role of gastric microbiota in gastric cancer – Stewart et al. – Gut Microbes

Ongoing Supplementation of Probiotics to Cesarean-Born Neonates during the First Month of Life may Impact the Gut Microbial – Yan et al. – Am J Perinatol

Animal experiments

Genetics but not intestinal microbiota determines the onset of systemic autoimmune disease in BXD2 mice – Hong et al. – The Journal of Immunology

Metabolic cooperation among commensal bacteria supports Drosophila juvenile growth under nutritional stress – Consuegra et al. – bioRxiv

Animal microbiome

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing – Mishra et al. – Archives of Microbiology

Microbial metabolomics

IBD Microbial Metabolome: The Good, Bad, and Unknown – Sidebottom and Chang – Trends in Endocrinology & Metabolism

Environmental microbiology

Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Dierent Conditions of Temperature, pH and CO – Xu et al. – Microorganisms

Plant, root, and soil microbiome

Livestock grazing abandonment reduces soil microbial activity and carbon storage in a Mediterranean Dehesa – Oggioni et al. – Applie Soil Ecology

Halotolerant plant growth–promoting bacteria: Prospects for alleviating salinity stress in plants – Etesami & Glick – Environmental and Experimental Botany

Fertilization changes soil microbiome functioning, especially phagotrophic protists – Zhao et a. – Soil Biology and Biochemestry

Effect of combined application of organic and inorganic phosphatic fertilizers on dynamic of microbial biomass in semi-arid soil – Khosa et al.- Soil Science Annual

High levels of primary biogenic organic aerosols are driven by only a few plant-associated microbial taxa – Abdoulaye et al. – Atmospheric Chemestry & Physics

Complexity of bacterial and fungal network increases with soil aggregate size in an agricultural Inceptisol – Liao et al. – Applied Soil Ecology

Azole use in agriculture reduces Aspergillus fumigatus abundance but does not alter its population structure – Barber et al. – bioRxiv

Food microbiology

Novel Approaches to Minimising Mycotoxin Contamination – Jovita and Nunez – Toxins

Mentholation triggers brand-specific shifts in the bacterial microbiota of commercial cigarette products – Malayil et al. – Applied Microbial and Cell Physiology

Good Saturday, everyone. Today the Microbiome Digest brings you the latest on plant-microbial interaction and environmental microbiology together with a variety of your usual microbiome related publications. Enjoy!.

Human respiratory microbiome

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation -Das et al.- bioRxiv

Human gut microbiome

A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities -Barlow et al.- Nature Communications

Gut Microbiota and Disorders of the Central Nervous System – Vuotto et al.- Neuroscientist

Animal experiments

Intestinal fungi are causally implicated in microbiome assembly and immune development in mice– Erik van Tilburg Bernardes et al.- Nature Communications

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea -Ma et a.- ISME

Built environment

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms -Fu et al.- mSystems

Environmental Microbiology

Extreme storms cause rapid, context-dependent shifts in nearshore subtropical bacterial communities -Ares et al.- bioRxiv

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase – Ballhausen et al.- Scientific Reports

Plant, root, and soil microbiome

Deciphering the root endosphere microbiome of the desert plant Alhagi sparsifolia for drought resistance-promoting bacteria -Zhang et al.- Applied and

Drought and plant litter chemistry alter microbial gene expression and metabolite production -Malik et al.- ISME

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium– DiCenzo et al.- Nature Communications

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

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