July 6, 2021

Several great papers today including a very interesting Cell paper on how Bifidobacterium interacts with the immune system and an mBio article on how different types of dietary fibre shape the gut microbiota.

To our Australian readers I’d like to wish a happy NAIDOC week, which is a time to celebrate the history, culture and achievements of Aboriginal and Torres Strait Islander peoples.

General microbiome

Microbiota regulate social behaviour via stress response neurons in the brain – Wu et al. Nature. 

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission – Bacci et al. Microbiome

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition. Cheng et al. mSystems

Human gut microbiome

Gut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice – Martin et al. Nature Communications. 

Gut microbes impact stroke severity via the trimethylamine N-oxide pathway – Zhu et al. Cell Host & Microbe

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities – Centu-Jungles et al. mBio

Pregnancy and Early-Life

Bifidobacteria-mediated immune system imprinting early in life – Henrick et al. Cell

Animal microbiome

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions – Lejal et al. Microbiome

Water Microbiome

Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions – Posadas et al. ISME

Soil microbiome

A Community Effort: Combining Functional Amplicon Sequencing and Metagenomics Reveals Potential Biosynthetic Gene Clusters Associated with Protective Phenotypes in Rhizosphere Microbiomes – Winter. mSystems.

Bioinformatics

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses – Milani et al. mSystems

June 8, 2021

Human gut microbiome

Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome – Bolte et al. Gut

Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy – Huang et al. Gut

Human skin microbiome

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching – Wilkins et al. Microbiome.

Animal microbiome

Host Species and Geography Differentiate Honeybee Gut Bacterial Communities by Changing the Relative Contribution of Community Assembly Processes – Ge et al. mBio

Animal experiments

Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells – Shmuel-Galia et al. Immunity

Water Microbiome

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. Microbiome

Phages and viruses

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases – Tisza and Buck. PNAS. 

Bioinformatics

A Critique of Differential Abundance Analysis, and Advocacy for an Alternative – Quinn et al. arXiv preprint. 

May 07, 2021

Human gut microbiome

Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome – Han et al. Microbiome

Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model – Newman et al. Microbiome

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models – Jiang et al. mSystems

Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential – Mangalea et al. Cell Host & Microbe. 

Human respiratory microbiome

Integrative microbiomics in bronchiectasis exacerbations – Mac Aogáin et al. Nature Medicine

Probiotics

The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics – Salminen et al. Nature Reviews Gastroenterology & Hepatology

Mycobiota/Fungi

Fungal taxonomy and sequence-based nomenclature – Lucking et al. Nature Microbiology

Host-Microbiota interactions

A Streptococcus Quorum Sensing System Enables Suppression of Innate Immunity – Rahbari et al. mBio

Bioinformatics

Tamock: simulation of habitat-specific benchmark data in metagenomics – Gerner et al. BMC Bioinformatics

Techniques

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota – Baker et al. Microbiome

March 16, 2021

Human gut microbiome

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles – Patnode et al. Cell Host & Microbe. 

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice – Jain et al. Science.

Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease – Dubinsky et al. mSystems

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. ISME

Early life 

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. ISME

Human oral microbiome

Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy – Wu et al. mSystems

Animal experiments 

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Yilmaz et al. Cell Host & Microbe

Bioinformatics

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data – Deng & Delart. BMC Bioinformatics

February 16th, 2021

Good afternoon from sunny Adelaide, Australia. Today’s digest highlights a range of interesting microbiome research, an article in Science modelling the future of SARS-CoV2, and a commentary in Cell on data sharing.

COVID-19

Immunological characteristics govern the transition of COVID-19 to endemicity – Lavine et al. Science.

Human gut microbiome

Can we modulate the breastfed infant gut microbiota through maternal diet? – Sindi et al. FEMS Microbiology Reviews. 

Impact of synbiotics on gut microbiota during early life: a randomized, double-blind study – Phavichitr et al. Scientific Reports

Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting – Amadi et al. Nature Microbiology

Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells – Iftekhar et al. Nature Communications

Animal experiments 

Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets –  Rosa et al. – mSystems

Human oral microbiome

Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes – Simon-Soro et al. npj biofilms and microbiomes

Marine  microbiome 

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort – Borchest et al. – mSystems

Phages and viruses

Balance between promiscuity and specificity in phage λ host range – Andrews and Fields – ISME

Bioinformatics

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets – Luca et al – ISME

A “data sharing trust” model for rapid, collaborative science – Chan et al. –  Cell

A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community – Joseph et al. – mSystems 

January 19, 2021

Today’s digest includes a full list of the collection of articles looking at the prenatal microbiota that was recently published in Microbiome as well as some excellent articles from Cell Host & Microbe. 

General Microbiome

A microbial metabolite remodels the gut-liver axis following bariatric surgery – Chaudhari et al. Cell Host & Microbe. 

[REVIEW] The microbiota in pneumonia: From protection to predisposition. Thibeault et al. Science Translational Medicine. 

Prenatal Microbiome

BMC Microbiome has published a collection of articles looking at the prenatal microbiome including perspectives, and commentaries from a range of experts.  

A philosophical perspective on the prenatal in utero microbiome debate – Walter and Hornef. Microbiome. 

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study – Goffau et al. Microbiome

Group therapy on in utero colonization: seeking common truths and a way forward. Silverstein and Mysorekar. Microbiome. 

Lessons learned from the prenatal microbiome controversy. Blaser et al. Microbiome. 

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – Fricke and Ravel. Microbiome. 

Corroborating evidence refutes batch effect as explanation for fetal bacteria – Rackeiyte et al. Microbiome

Gut microbiome

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Tanes et al. Cell Host & Microbe

Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System – Amenyogbe et al. mSystems

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy – He et al. mSystems

Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions – Sharma et al. mSystems

Animal microbiome

Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens –  Ding et al. mSystems 

Probiotics

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice – Lee et al. Nature Microbiology. 

December 7, 2020

Today we have some excellent review articles in Science, and Gut as well as several interesting research articles.

COVID-19 

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms – Gordon et al. Science

Robust neutralizing antibodies to SARS-CoV-2 infection persist for months – Wajnberg et al. Science

General Microbiome

[REVIEW] The role of the microbiota in human genetic adaptation – Suzuki and Ley – Science 

Gut microbiome

Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism – Penney et al. mSystems

[REVIEW] Gut microbiota-derived metabolites as central regulators in metabolic disorders – Agus et al. Gut

Human respiratory microbiome

[REVIEW]  Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways. Khanolkar et al. mSystems

Animal microbiome

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen – Gharechahi et al. ISME

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks – Fan et al. BMC Microbiology

Bioinformatics

[REVIEW]  Analysis of microbial compositions: a review of normalization and differential abundance analysis – Lin and Peddada. Npj Biofilms and Microbiomes. 

Non-microbiome pick 

A comparative genomics multitool for scientific discovery and conservation – Zoonomia Consortium. Nature

November 4, 2020

Some very nice articles in todays digest including a probiotic study in Science Translation Medicine and a non-microbiome pick for dog lovers at the end. Enjoy!

COVID-19 & Vaccines

SARS-CoV-2 viral load is associated with increased disease severity and mortality – Fajnzylber et al. Nature Communications

Gut microbiome

Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites – Guo et al. Science

Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice – Khan et al. Science Translational Medicine

Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions – Bojar et al. Cell Host & Microbe

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations – Pruss et al. ISME

Microbiota-Derived Short-Chain Fatty Acids Promote LAMTOR2-Mediated Immune Responses in Macrophages – Wu et al. mSystems

Probiotics

A probiotic yeast-based immunotherapy against Clostridioides difficile infection – Chen et al. Science Translational Medicine

Water and extremophile microbiome

Host specificity of microbiome assembly and its fitness effects in phytoplankton – Jackrel et al. ISME

Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge) – Lecoeuvre et al. ISME

Phages and viruses

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics – Arbas et al. Nature Microbiology

Bioinformatics

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons – Wei et al. Bioinformatics

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes – Gruber-Vodicka et al. mSystems

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity – Youngblut et al. mSystems

Non-microbiome pick 

Origins and genetic legacy of prehistoric dogs – Berstrom et al. 

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

Bioinformatics

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