May 5, 2023

Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome


Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

April 19, 2023

Pregnancy and early life

[REVIEW]The maternal gut microbiome during pregnancy and its role in maternal and infant health – Sinha et al. – Current Opinion in Microbiology

Human oral microbiome

Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses – Beall et al. – mBio

[REVIEW]Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review – Lin et al. – Clinical Oral Investigations

Human vaginal microbiome

[REVIEW]Gardnerella Revisited: Species Heterogeneity, Virulence Factors, Mucosal Immune Responses, and Contributions to Bacterial Vaginosis – Shvartsman et al. – Infection and Immunity

Human gut microbiome/virome

[REVIEW]Intrahost evolution of the gut microbiota – Barreta & Gordo – Nature Reviews Microbiology

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice – Fan et al. – Nature Microbiology

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori – Wang et al. – Nature Communications

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Spatz et al. – Microbiome

Metabolic independence drives gut microbial colonization and resilience in health and disease – Watson et al. – Microbiome

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty – Ou et al. – European Child & Adolescent Psychiatry

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals – Segota et al. – NAR

Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease – Poudel et al. – PLOS One

Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease – Tani et al. – PLOS One

The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study – Oh et al. – Journal of Translational Medicine volume

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

Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus) – Taylor et al. – Journal of the American Association for Laboratory Animal Science

Music-based interventions in the feeding environment on the gut microbiota of mice – Niu et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality – Maidment et al. – Microbiome

[PREPRINT]Microbiome variability of mosquito lines is consistent over time and across environments – Accoti et al. – bioRxiv

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus) – Wei et al. – Applied Microbiology and Biotechnology


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Bazant et al. – Microbiome


Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle – Liu et al. – Microbiome

April 14, 2023

Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Madeleine Spatz – Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe


Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

March 8, 2023

Pregnancy and early life

[PREPRINT]The influence of early life exposures on the infant gut virome – Zhang et al. – bioRxiv

[PREPRINT]Maternal diet and gut microbiome composition modulate early life immune responses – Grant et al. – bioRxiv

Human oral microbiome

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease – Tamashiro et al. – Scientific Reports

Human gut microbiome

Gut microbiota and risk of five common cancers: A univariable and multivariable Mendelian randomization study – Wei et al. – Cancer Medicine

The role of the sex hormone-gut microbiome axis in tumor immunotherapy – Wang et al. – Gut Microbes

[REVIEW]The Influence of the Microbiome on Aggressive Behavior: an Insight into Age Related Aggression – Gulledge, Oyebode & Donaldson – FEMS Microbiology Letters

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

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity – Daoust et al. – Gut

Animal microbiome (for animals in the wild)

[REVIEW]The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions – Mohamed et al. – FEMS Microbiology Reviews

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet – Feng et al. – Front. Vet. Sci.

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

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function – Shi et al. – BMC Microbiology

Species invasions shift microbial phenology in a two-decade freshwater time series – Rohwer et al. – PNAS


Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – BMC Microbiology

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies – Luz Calle, Pujolassos & Susin – BMC Bioinformatics

[PREPRINT]You can move, but you can’t hide: identification of mobile genetic elements with geNomad – Camargo et al. – bioRxiv

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing – Wick, Judd & Holt – PLOS Computational Biology

February 25th, 2023

Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! Fontana and collaborator performed a fascinating meta-analysis of publicly datasets obtained from fecal samples of healthy athletes and healthy sedentary adults and revealed the microbiota changes associated with competitive athletes lifestyle.

Today’s non-microbiology pick is an preprint exploring postdoctoral and PhD student’s career self-efficacy in US biological sciences and showed how women and non US citizen have a significant lower level of career self-efficacy compared to their male and US citizen peers. The authors discuss potential causes for these differences and offer recommendations for increasing trainee career self-efficacy.

Have a great Saturday!

Pregnancy and early life

Preprint: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Li et al. – BioRXiv

Human gut microbiome

The human gut microbiome of athletes: metagenomic and metabolic insights – Fontana et al. – Microbiome

Review: Gut microbiome-based strategies for host health and disease – Wang et al. – Critical Reviews in Food Science and Nutrition

The role of diet in shaping human gut microbiota – Rinninella et al. – Best practive & Research clinical Gastroenterology

Preprint: Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Robitaille et al. – BioRXiv

Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups – Wei et al. – Foods

Animal microbiome

Preprint: Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) – Andres et al. – BioRXiv

Plant, root, and soil microbiome

Preprint: Short- and long-term effects of continuous compost amendment on soil microbiome community – Kraut-Cohen et al. – BioRXiv

Awaking the Dormant Virome in the Rhizosphere – Braga and Schumacher – Molecular ecology

Water and extremophile microbiome

Preprint: A novel order-level lineage of ammonia-oxidizing Thaumarchaeota is widespread in marine and terrestrial environments – Zheng et al. – BioRXiv

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics – Dart et al. – Viruses

Food microbiology

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica) – Hines et al. – Plos One

Phages and viruses

Review: The Role of Temperate Phages in Bacterial Pathogenicity – Gummalla et al. – Microorganisms


Review: Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses – Ibanez-Lligona et al – Viruses

Non microbiology pick

Preprint: Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States – Chatterjee et al. – BioRXiv

February 18th, 2023

Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! An amazing read is a fresh preprint from Fritz and collaborator describing an exciting method of sampling in difficult to reach environments. The authors used army ants of the genus Dorylus which are foragers to survey the viral diversity of plants, vertebrate and invertebrates of the tropical forest!

Today’s non-microbiology pick is an opinion piece on the current state and limitation of viral taxonomy. In this piece, Simmonds and collaborators, provide concrete recommendations to guide the development of a coherent and comprehensive virus taxonomy.

Have a great Saturday!

Pregnancy and early life

The investigation of the association of pregnancy weight gain on maternal and neonatal gut microbiota composition and abundance using 16sRNA sequencing – Song and Liu – BMC Pregnancy and Childbirth

Human gut microbiome

The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population – Bourdeau-Julien et al. – Microbiome

Review: Conversations in the Gut: The Role of Quorum Sensing in Normobiosis – Markus et al. – International Journal of Molecular Sciences

Review: Gut Microbiome and Neurodevelopmental Disorders: A Link Yet to Be Disclosed – Illiodromiti et al. – Microorganisms

Natural Green Spaces, Sensitization to Allergens, and the Role of Gut Microbiota during Infancy – Buchholz et al. – mSystems

Animal experiments

Mimicking seasonal changes in light-dark cycle and ambient temperature modulates gut microbiome in mice under the same dietary regimen – Matsumoto et al – Plos One

Animal microbiome

Preprint: Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta – Moeller et al. – BioRxiV

Plant, root, and soil microbiome

Preprint: Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype – Simonin et al. – BioRxiV

Preprint: Viral but not bacterial community succession is characterized by extreme turnover shortly after rewetting dry soils – Santos-Medellin et al. – BioRxiV

Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils – Gao et al. – Science of the total environment

Water and extremophile microbiome

Preprint: Redefinition of archetypal phytoplankton-associated bacteria taxa based on globally distributed dinoflagellates and diatoms – Yang et al. – BioRxiV

Preprint: Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities – Vlaanderen et al. – BioRxiV

Phages and viruses

Preprint: African army ants at the forefront of virome surveillance in a remote tropical forest – Fritz et al. – BioRxiV


Preprint: Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction – Simon et al. – BioRxiV

Preprint: The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies – Cook et al. – BioRxiV

Non microbiology pick

Opinion: Four principles to establish a universal virus taxonomy – Simmonds et al. – PLoS Biology

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