October 6, 2020

Starting today’s digest with a couple of very interest studies on COVID-19 in Nature and Science. There’s also multiple interesting virome papers today.

COVID-19 & Vaccines

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans – Mateus et al. Science

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals – Zeberg et al. Nature

Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR – Smyrlaki et al. Nature Communications. 

General microbiome

Identification of new enterosynes using prebiotics: roles of bioactive lipids and mu-opioid receptor signalling in humans and mice – Abot et al. Gut

Assessing the Variation within the Oral Microbiome of Healthy Adults – Nearing et al. mSphere

Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes – Schmidt et al. mSystems

Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces – Ghimire et al. PeerJ.

Gut microbiome

Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD – Lee et al. Nature Communications

Animal microbiome 

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet – Bermudez-Sanchez. PeerJ

Plant microbiome

Achieving similar root microbiota composition in neighbouring plants through airborne signalling – Kong et al. ISME

Phages and viruses

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization – Zuo et al. Cell Host & Microbe

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity – Meaden et al. ISME

Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy – Bajaj et al. Gut

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes – Shi et al. mSystems

September 3, 2020

At the beginning of todays post I wanted to highlight some interesting recent articles on COVID-19 and in particular a recent trial demonstrating the utility of BCG for a trained immunity response to protect against respiratory infections in the elderly. Enjoy!

COVID-19 & Vaccines

Tracking the COVID-19 pandemic in Australia using genomics – Seemann et al. Nature Communications. 

A comparison of four serological assays for detecting anti–SARS-CoV-2 antibodies in human serum samples from different populations – Grzelak et al. Science Translational Medicine

Phase 1–2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine – Keech et al. New England Journal of Medicine

ACTIVATE: Randomised clinical trial of BCG vaccination against infection in the elderly – Giamarellos-Bourboulis et al. Cell


General microbiome

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease – Bushman et al. Cell Host & Microbe

Gut mycobiome and its interaction with diet, gut bacteria and alzheimer’s disease markers in subjects with mild cognitive impairment: A pilot study – Nagpal et al. EBioMedicine

Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Fontaine et al. PLOS One

Human respiratory microbiome

Respiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A Virus – Rowe et al. mSystems

Animal microbiome

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia – Shanmuganandam et al. PeerJ

Water and extremophile microbiome

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters – Marchioro et al. PeerJ

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth – Miller et al. mBio. 

Phages and viruses

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts – Fujimoto et al. Cell Host & Microbe


BLAST-QC: automated analysis of BLAST results – Torkian et al. Environmental Microbiome


August 5, 2020

Today’s Microbiome Digest showcases a study of a microbiota derived metabolite that promotes HDAC3 in the gut indicating an epigenetic senror of the microbiota, as well as several interesting papers from Cell Host & Microbe, Nature Microbiology and mSystems.


Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic – Boni et al. Nature Microbiology

Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients – Wang et al. Cell Host & Microbe

General microbiome

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Kim et al. BMC Microbiome. 

Microbiota-derived metabolite promotes HDAC3 activity in the gut – Wu et al. Nature


Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis – Bellerose et al. mSystems

Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis – Quigley et al. mBio


Water and extremophile microbiome

Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem – Trivedi et al. mSystems


Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. Nov. – Wu et a. mSystems

Phages and viruses

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome – Wolf et al. Nature Microbiology

July 3rd, 2020

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology


ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics


High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems

June 4, 2020

General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

Human microbiome

Review – Host–microbiota interactions in immune-mediated diseases. Ruff et al. – Nature Reviews Microbiology

Human gut microbiome

Gut microbial diversity, inflammation, and oxidative stress are associated with tacrolimus dosing requirements early after heart transplantation – Jennings et al. PLOS One

Review – Interaction between drugs and the gut microbiome – Weersma et al. – Gut

Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship – Yuan et al. mSystems

Animal microbiome

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance – Barelli et al. mSystems.

Plant, root and soil microbiome

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation – Carrion et al. Microbiome


Probiotics for the prevention of antibiotic-associated adverse events in children—A scoping review to inform development of a core outcome set – Lukasik et al. –  PLOS One

Phages and viruses

Predicting host taxonomic information from viral genomes: A comparison of feature representations – Young et al. PLOS Comp Biology. 

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Moon et al. Microbiome.


The hidden layers of microbial community structure: extracting the concealed diversity dimensions from our sequencing data – Fasolo et al. – FEMS Microbiology Letters

Compositional Lotka-Volterra describes microbial dynamics in the simplex – Joseph et al. PLOS Computational Biology.


Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing – Blattman et al. – Nature Microbiology.

May 6, 2020

General microbiome

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome – Rifkin et al – Microbiome

The neovaginal microbiome of transgender women post-gender reassignment surgery  – Birse et al – Microbiome

Pregnancy and early life

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang et al – Nature

Human gut microbiome

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study – Harakeh et al – PLOS One

Animal experiments

Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization – Yeung et al – Cell Host & Microbe

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al – Microbiome

Vitamin D receptor promotes healthy microbial metabolites and microbiome – Chatterjee et al – Nature Scientific Reports

Phages and viruses

Phages Actively Challenge Niche Communities in Antarctic Soils – Bezuidt et al – mSystems


The Syntrophy hypothesis for the origin of eukaryotes revisited – López-García & Moreira – Nature Microbiology

Microbes in the news

State-of-the-art imaging method provides new insights into how bacteria move and exchange genetic information

April 2, 2020

Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

Lung function and microbiota diversity in cystic fibrosis – Cuthbertson et al. – BMC Microbiome

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Yu et al. – PLOS Medicine

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports


Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports