February 4th, 2023

Bonjour from Paris, France !

In today’s digest you will find a wide variety of interesting preprints and published research papers encompassing very interesting microbiome such as Yak calves rumen, compost, wineyard soil and lichen symbionth microbiota!

If you are interested in virome, I recommend looking at the fascinating preprint from Ha and collaborators investigating the biogeography of giant viruses from the phylum Nucleocytoviricota. They leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to recovered novel genomes from these viruses and identified geographical patterns of distribution.

If you are working on human microbiomes, I recommend checking out a really interesting preprint, comparing the biases and strengths of four commercially available DNA extraction kits frequently used for whole genome shotgun analysis of the human microbiome.

Have a great Saturday!

Events and jobs

Event: Cell Symposia: Infection biology in the age of the microbiome. Paris, France June 7-9

Event: 55th Annual Meeting of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition. Vienna, Austria 17-20 May

Pregnancy and early life

Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study – Leech et al. – Nutrients

Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota – Morreale et al. – Antibiotics

Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites – Kaplina et al. – International Journal of Molecular sciences

Human gut microbiome

Preprint: Functional assignment of gut-specific archaeal proteins in the human gut microbiome – Novikova et al. – BioRxiv

Animal microbiome

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea – Woo et al. – PLOS ONE

The association between gingivitis and oral spirochetes in young cats and dogs – Yamaki et al. – PLOS ONE

Maternal rumen and milk microbiota shapes the establishment of early-life rumen microbiota in grazing yak calves – Guo et al. – Journal of Dairy Science

Plant, root, and soil microbiome

Preprint: Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding – Hendiani et al. – BioRxiv

Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards – Steiner et al. – PLOS ONE

Preprint: Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes – Tagirdzhanova et al. – BioRxiv

Water and extremophile microbiome

Preprint: Assessing the biogeography of marine giant viruses in four oceanic transects – Ha et al. – BioRxiv

Preprint: Cross-domain interactions induce community stability to benthic biofilms in proglacial streams – Busi et al. – BioRxiv

Opinion: Viral infection in the ocean—A journey across scales – Vincent and Vardi – PLOS biology


Preprint: Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome – Van Dijk et al – BioRxiv


Preprint: Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples – Wright et al – BioRxiv

January 27, 2023

General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME


Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

November 09, 2022

General microbiome

Compartmentalization of the host microbiome: how tumor microbiota shapes checkpoint immunotherapy outcome and offers therapeutic prospects – Boesch et al. – Journal for ImmunoTherapy of Cancer

Human respiratory microbiome

The Upper-Airway Microbiome as a Biomarker of Asthma Exacerbations despite Inhaled Corticosteroid Treatment – Perez-Garcia – Journal of Allergy and Clinical Immunology

Human gut microbiome

Manipulating the microbiome to enhance oral tolerance in food allergy – Gonzalez-Visiedo – Cellular Immunology

Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis – Bajaj et al. – Hepatology

Happy ageing by trusting our gut microbes – Jayaraman & Pettersson – Biochemical and Biophysical Research Communications

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Curcumin improves insulin sensitivity in high-fat diet-fed mice through gut microbiota – Zhong et al. – Nutrition & Metabolism

Short-Term Tomato Consumption Alters the Pig Gut Microbiome toward a More Favorable Profile – Goggans et al. – Microbiology Spectrum

[PREPRINT]Lifelong temporal dynamics of the gut microbiome associated with longevity in mice – Takayasu et al. – bioRxiv

[PREPRINT]The gut microbiome has sexually dimorphic effects on bone tissue energy metabolism and multiscale bone quality in C57BL/6J mice – Vahidi et al. – bioRxiv

Animal microbiome (for animals in the wild)

Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome – Li et al. – Science of The Total Environment

Phages and viruses

Expansion of the global RNA virome reveals diverse clades of bacteriophages – Neri et al. – Cell


C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data – Song & Zhou – BMC Bioinformatics

September 9, 2022

The #MVIF Season 2 is starting NEXT WEEK!

With the new starting time to better accommodate extra time zones &
highlights will be hosted by @gather_town for more engaging personal interaction & networking (from October).


Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation – Allison K. Guitor – Microbiome

Review: Soil microbiomes and one health – Samiran Banerjee & Marcel G. A. van der Heijden – Nature Reviews Microbiology

Oral microbiome

Corncob structures in dental plaque reveal microhabitat taxon specificity – Viviana Morillo-Lopez – Microbiome

Vaginal microbiome

Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy – Kathryn E.McCauley – Cell Reports Medicine

Gut virome/microbiome

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort – Suguru Nishijima – Nature Communications

Review: Mutualistic interplay between bacteriophages and bacteria in the human gut – Andrey N. Shkoporov – Nature Reviews Microbiology

Identification of trypsin-degrading commensals in the large intestine – Youxian Li – Nature

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Yoshinaga Kawano – Cell

Design, construction, and in vivo augmentation of a complex gut microbiome – Alice G. Cheng – Cell

Plant, root and soil microbiome

Source and acquisition of rhizosphere microbes in Antarctic vascular plants – Sergio Guajardo-Leiva – Frontiers in Microbiology

Animal microbiome

Individual variation in the avian gut microbiota: the influence of host state and environmental heterogeneity – Shane E. Somers – bioRxiv

Animal experiment

From germ-free to wild: modulating microbiome complexity to understand mucosal immunology – Carolyn A. Thomson – Mucosal Immunology

August 03, 2022

Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology


Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

July 12, 2022

Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution


Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association

June 15, 2022

General microbiome

[PREPRINT]Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica – Escudero-Leyva et al. – bioRxiv

Pregnancy and early life

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life – Wells et al. – Annual Review of Nutrition

Multi-site human microbiome

A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao – Han et al. – Clinical and Translational Medicine

Human oral microbiome

The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine – Herremans et al. – Microbiome

Human skin microbiome

Altered skin fungal and bacterial community compositions in tinea capitis – Rong et al. – Mycoses

Effects of short chain fructo-oligosaccharides on selected skin bacteria – Le Bourgot et al. – Scientific Reports

Human vaginal microbiome

Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome – Ruotsalainen et al. – Medical Microbiology and Immunology

Human gut microbiome

Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients – Hoang et al. – BMC Cancer

Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study – Miao et al. – BMC Medicine

[REVIEW]The role of virome in the gastrointestinal tract and beyond – Tiamani et al. – FEMS Microbiology Reviews

[REVIEW]Time-limited diets and the gut microbiota in cardiometabolic disease – Ratiner et al. – Journal of Diabetes

Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial – Huang et al. – Journal of Autoimmunity

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer – Fu et al. – Cell

Pharmacokinetic and gut microbiota analyses revealed the effect of Lactobacillus acidophilus on the metabolism of Olsalazine in ulcerative colitis rats – Li et al.

Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis – Forster et al. – Nature Microbiology

Plant, root, and soil microbiome

The plant host environment influences competitive interactions between bacterial pathogens – Ehau-Taumaunu & Hockett – Environmental Microbiology Reports


[PREPRINT]specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data – Darcy et al. – bioRxiv

June 01, 2022

General microbiome

[REVIEW]Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms – Cani et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Role of Microbiota in Viral Infections and Pathological Progression – Mizutani et al. – Viruses

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Newbury et al. – PNAS

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales – Martinez-Gutierrez & Aylward – PLOS Genetics

Interspecies commensal interactions have nonlinear impacts on host immunity – Rice et al. – Cell Host & Microbe

Human skin myco-/microbiome

Distinct skin microbiome community structures in congenital ichthyosis – Tham et al. – British Journal of Dermatology

Biodiversity of mycobial communities in health and onychomycosis – Olbrich et al. – Scientific Reports

Human gut microbiome

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study – Jiang et al. – Genome Medicine

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. – Cell Host & Microbe

Discovery of bioactive microbial gene products in inflammatory bowel disease – Zhang et al. – Nature

Animal microbiome (for animals in the wild)

The functional evolution of termite gut microbiota – Arora et al. – Microbiome

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods – Oba et al. – Journal of Animal Science

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth – Zhang et al. – Front. Microbiol.

Plant, root, and soil microbiome

Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships – Schäfer et al. – Nature Microbiology

Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis – Mehlferber et al. – Current Biology

May 25, 2022

General microbiome

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness – Ørsted et al. – PLOS Genetics

Human skin microbiome/virome

[PREPRINT]Diversity, abundance, and host specificity of the human skin associated circular and single stranded DNA virome – Graham et al. – bioRxiv

[REVIEW]Climate change, the cutaneous microbiome and skin disease: implications for a warming world – Isler et al. – International Journal of Dermatology

Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects – Benitez-Paez et al. – Gut Microbes

Human gut microbiome

[PREPRINT]Greater alteration of gut microbiota occurs in childhood obesity than adulthood obesity – Yu et al. – bioRxiv

Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet – Dahlin et al. – eBioMedicine

Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome – Liu et al. – Front. Microbiol.

Animal microbiome (for animals in the wild)

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing – Que et al. – Front. Cell. Infect. Microbiol.

Bacterial Adaptation to Venom in Snakes and Arachnida – Esmaeilishirazifard et al. – Microbiology Spectrum

Plant, root, and soil microbiome

Recent advances in understanding of fungal and oomycete effectors – Wilson & McDowell – Current Opinion in Plant Biology

Fungi associated with the potato taste defect in coffee beans from Rwanda – Hale et al. – Botanical Studies

Delineating the Bacteriome of Packaged and Loose Smokeless Tobacco Products Available in North India – Srivastava et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding – de Souza et al. – Scientific Reports

May 11, 2022

General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv


Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment