May 8th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers, in particular in bioinformatics! I recommend anyone interesting in metagenomic read classification to take a look at the benchmark study by Arizmendi Cardenas and collaborators. They compared read-based taxonomic classification tools on their capacity to handle ancient DNA sequences, characterized by a higher mutation rate and shorter sequences.

This digest also contains a very good review on the current state of the art network analysis methods for exploring interaction in complex microbial communities.

Finally, today’s non-microbiology pick is a piece exploring the current challenges and limitations for the annotation of microbiome dataset with high-quality metadata.

Have a great Weekend!

Human gut microbiome

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease – Aldars-Garcia et al. – Microorganisms

Animal experiments

Millet-based supplement restored gut microbial diversity of acute malnourished pigs – Li et al. – PLOS One

A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets – Miragoli et al. – PLOS One

Animal microbiome

Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging – Tan et al. – Microbiology Open

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France – Nebbak et al. – Viruses

Plant, root, and soil microbiome

Preprint: Mapping the microbial diversity and natural resistome of north Antarctica soils – Marcoleta et al. – BioRXiv

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments – Ma et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Book chapter: Bioprospecting Extreme Ecosystems Before They Vanish: The (Poorly Studied) Microbiology of Tropical Glaciers – Yarzabal – Extreme environment (CRC press)

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores – Pearman et al. – PLOS One


Preprint: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study – Arizmendi Cardenas et al. – BioRXiv

Review: Network analysis methods for studying microbial communities: A mini review – Matchado et al. – Computational and sctructural Biotechnology Journal

Improving metagenomic binning results with overlapped bins using assembly graphs – Mallawaarachchi et al. – Algorithms for molecular biology

My non-microbiology picks

Preprint: Current challenges in microbiome metadata collection – Rosenfeld et al. – BioRXiv

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


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


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


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


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

May 4, 2021

In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal


Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology


Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications

May 1, 2021

Have a great International Workers’ Day! Today, in this Digest: a review article about the role of butyrate (a product of microbiome activity) in the early development of microbiota. We have also: probiotics and COVID19, microbiota toxins and cardiovascular disease, microbiome studies from Indonesia, a US cohort study investigating links between the microbiome, diet, and TMAO levels; several articles about connections between the diet and the microbiome, shrimp microbiota, and more!   

Human and General Microbiome

Review: Microbial driven genetic variation in holobionts – Ilana Zilber-Rosenberg and Eugene Rosenberg – FEMS Microbiology Reviews

Review: Butyrate: A Link between Early Life Nutrition and Gut Microbiome in the Development of Food Allergy – Margherita Di Costanzo et al.,Life (MDPI)

Review: Next-Generation Probiotics and Their Metabolites in COVID-19 – Thomas Gautier et al.,Microorganisms (MDPI)

Review: Circulating bile acids as a link between the gut microbiota and cardiovascular health: Impact of Prebiotics, probiotics and polyphenol-rich foods – R.A.G. Pushpass et al., – Nutrition Research Reviews

Review: Two Gut Microbiota-Derived Toxins Are Closely Associated with Cardiovascular Diseases: A Review – Tomoya Yamashita et al., – Toxins (MDPI)

Review: Dietary Strategies for Management of Metabolic Syndrome: Role of Gut Microbiota Metabolites – Sonia Croci et al., – Nutrients (MDPI)

Review: Challenging Cosmetic Innovation: The Skin Microbiota and Probiotics Protect the Skin from UV-Induced Damage – Djouhar Souak et al., – Microorganisms (MDPI)

Perspective: Gut microbiota through an evolutionary lens – Rachel N. Carmody et al., – Science

Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta – Phatthanaphong Therdtatha et al., – Microorganisms (MDPI)

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li et al., – Gut (BMJ)

Isolation and identification of a human intestinal bacterium capable of daidzein conversion – Yingyu Guo et al., FEMS Microbiology Letters

Associations of fine particulate matter and its constituents with airway inflammation, lung function, and buccal mucosa microbiota in children – Yihan Wu et al., – Science of The Total Environment

Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease – Claire Healy et al., – Respiratory Research (BMC)

Gut bacterial profile in Indian children of varying nutritional status: a comparative pilot study – Chandrasekhar Balasubramaniam et al., European Journal of Nutrition

The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro – Shanthi G. Parkar et al., – Scientific Reports

Oral-Gut Microbiome Axis in Gastrointestinal Disease and Cancer – Se-Young Park et al.,cancers (MDPI)

Effects of Whole-Grain and Sugar Content in Infant Cereals on Gut Microbiota at Weaning: A Randomized Trial – Julio Plaza-Diaz et al., – Nutrients (MDPI)

Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study – Annamaria Altomare et al., – Nutrients (MPDI)

Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid – Sa-Ra Lee et al., – International Journal of Molecular Sciences


A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor – Jay Vornhagen et al.,PLoS Pathogens

Animal Microbiome

Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community – Quentin Lamy-Besnier et al.,Microbiology Resource Announcements

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters – Rodrigo García-López et al., – Genes (MDPI)

Plant Microbiome

Impact of pesticide/fertilizer mixtures on the rhizosphere microbial community of field-grown sugarcane – Weijuan Huang et al.,3 Biotech 

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts – Milada Solcova et al., – Microorganisms (MDPI)

Food Microbiome

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing – Reid G. Griggs et al., – Frontiers in Microbiology

Other Microbes

Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness – Tomer Orevi and Nadav Kashtan – Frontiers in Microbiology

Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station – Anna C. Simpson et al.,Microbiology Resource Announcements

April 28, 2021

General microbiome

Microbiota regulate innate immune signaling and protective immunity against cancer – Xing et al. – Cell Host & Microbe

Pregnancy and early life

[PREPRINT]Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants – Yan et al. – bioRxiv

[REVIEW]Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review – Zaidi, Moore & Okala – Nutrients

Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle – Seppo et al. – Allergy

Human skin microbiome

Can antibiotic‐induced changes in the composition of the hair follicle microbiome regulate human hair growth? – Lousada et al. – Experimental Dermatology

Human gut microbiome

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome – Hu et al. – Theranostics

Alteration of gut microbial profile in patients with diabetic nephropathy – Du et al. – Endocrine

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

Sargassum fusiforme fucoidan modifies gut microbiota and intestinal metabolites during alleviation of hyperglycemia in type 2 diabetic mice – Wu et al. – Food & Function

Bidirectional interaction of nobiletin and gut microbiota in mice fed with a high-fat diet – Zhang et al. – Food & Function

Reshaping of the gastrointestinal microbiome alters atherosclerotic plaque inflammation resolution in mice – Garshick et al. – Scientif Reports

Animal microbiome (for animals in the wild)

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits – Zheng et al. – PLOS One

Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone – Antwis et al. – Journal of Animal Ecology

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

[PREPRINT]A Scenic River in Rural Ohio Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy et al. – bioRxiv

[PREPRINT]Diversity of free-living prokaryotes on terrestrial and marine Antarctic habitats – Bendia et al. – bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics – Cabello-Yeves – Environmental Microbiome


Obtaining deeper insights into microbiome diversity using a simple method to block host and non‐targets in amplicon sequencing – Mayer et al. – Molecular Ecology Resources

April 26, 2021

Greetings from Pittsburgh! Today’s digest is preprint heavy. Topics include an optimized protocol for cyanobacterial 16S rRNA analysis, a panel of Pseudomonas aeruginosa clinical isolates, and more! Happy reading!

Events and jobs

The National Summer Undergraduate Research Project is looking for microbiology or computational immunology grad trainees, postdocs, staff scientists, and group leaders to serve as mentors for their summer program. Sign up here!

General microbiome

Preprint: A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development – Lebreton et al. – bioRxiv

Pregnancy and early life

Preprint: Diet potentially drives the differentiation of eating behaviours via alterations to the gut microbiome in infants – Yan et al. – bioRxiv

Multi-site human microbiome

An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer – Borchmann – Microbiome

Plant, root, and soil microbiome

Preprint: Transcription of macromolecular N degrading genes provides a window into organic nitrogen decomposition in soil – Sieradzki et al. – bioRxiv

Built environment

Preprint: Microbial biomass, composition, and functions are responsible for the differential removal of trace organic chemicals in biofiltration systems – Cao et al. – bioRxiv
Microbes in space

Food microbiology

Preprint: Fluoroquinolone-resistant Escherichia coli originating on dairy farms are an infrequent cause of bacteriuria in humans living in the same geographical region – Mounsey et al. – bioRxiv


Preprint: Optimized protocol for Cyanobacterial 16S rRNA analysis in Danube Delta lakes – Moza & Postolache – bioRxiv

April 24th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.

Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!

Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.

Have a great Weekend!

General microbiome

Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology

Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV

Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos

Human gut microbiome

Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV

Animal experiments

Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control

Animal microbiome

Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal

Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports

Water and extremophile microbiome

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal

Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal

Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV


Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One

A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports


Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV

My non-microbiology picks

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database

April 21, 2021

General microbiome

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection – Mu et al. – Microbiome

Pregnancy and early life

A Microbiota-Directed Food Intervention for Undernourished Children – Chen et al. – The New England Journal of Medicine

Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life – Boutin et al. – eLife

Human vaginal microbiome

[REVIEW]The effect of different contraceptive methods on the vaginal microbiome – Bastianelli et al. – Expert Review of Clinical Pharmacology

Human gut microbiome and virome

The Gut Microbiome in Progressive Multiple Sclerosis – Cox et al. – Annals of Neurology

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity – Zuo et al. – Microbiome

[REVIEW]The Gut Microbiome: a New Frontier in Musculoskeletal Research – Li et al. – Current Osteoporosis Reports

[REVIEW]Inflammation‐driven brain and gut barrier dysfunction in stress and mood disorders – Doney et al. – European Journal of Neuroscience

The gut microbiota is associated with clinical response to statin treatment in patients with coronary artery disease – Wang et al. – Atherosclerosis

[REVIEW]Dietary restrictions modulate the gut microbiota: Implications for health and disease – Schmidt and Lorentz – Nutrition Research

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

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma – Chen et al. – Cancer Research

Screening of probiotic candidates in a simulated piglet small intestine in vitro model – Hansen et al. – FEMS Microbiology Letters

Animal microbiome (for animals in the wild)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history – Carrier et al. – PNAS

[PREPRINT]Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections – Mounsey et al. – bioRxiv

Diversity structure of the microbial communities in the guts of four neotropical termite species – Vikram et al. – PeerJ

Alteration of gut microbiota with a broad‐spectrum antibiotic does not impair maternal care in the European earwig – van Meyel et al. – Journal of Evolutionary Biology

Food microbiology

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites – Sawada et al. – PeerJ


[PREPRINT]Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach – Sengupta et al. – bioRxiv

April 16, 2021

In today’s digest read about the presence/absence of ACBP orthologues in human gut metagenomes and how the gut microbiome links nutrition with cardiometabolic health, LEGO-based microscope, SIAMCAT for statistical inference of associations between microbial communities and host phenotypes, bacteriophage plaques size tool, and more. Check out a list of awesome webinars and courses. Happy Friday!

OPEN #NSURP2021 CALL for mentors and mentees: The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.

Microbiome in the news

*Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo and Gonzalo Casino – PlosOne


Prokaryotic taxonomy and nomenclature in the age of big sequence data – Philip Hugenholtz – The ISME Journal

The metabolic network of the last bacterial common ancestor – Joana C. Xavier – Communications Biology


*Designing a high-resolution, LEGO-based microscope for an educational setting – Bart Eduard Vos – bioRxiv

Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay – Jacquelynn Benjamino – mSphere

Gut microbiome

*Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity – Andrew Maltez Thomas – Applied and Environmental Microbiology

The long-term genetic stability and individual specificity of the human gut microbiome – Lianmin Chen – Cell

Review: Emulating the gut–liver axis: Dissecting the microbiome’s effect on drug metabolism using multiorgan-on-chip models – Mara Lucchetti – Current Opinion in Endocrine and Metabolic Research

Urinary microbiome

The human urobiome – Linda Brubaker – Mammalian Genome

Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods – Baylie R. Hochstedler – International Urogynecology Journal

Vaginal microbiome

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil – Marcelle Oliveira de Almeida – PeerJ

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment – Leonardo Mancabelli – Applied and Environmental Microbiology


Review: Lacticaseibacillus rhamnosus GR-1, a.k.a. Lactobacillus rhamnosus GR-1: Past and Future Perspectives – Mariya I.Petrova – Trends in Microbiology

Probiotic Lactobacillus sp. Strains Inhibit Growth, Adhesion, Biofilm Formation, and Gene Expression of Bacterial Vaginosis-Inducing Gardnerella vaginalis – Zhixiang Qian – Microorganisms

Oral microbiome

Dental biofilm microbiota dysbiosis is associated with the risk of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation – Vitor Heidrich – medRxiv

Soil microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Carla Perez-Mon – Microbial Genomics

Phages and viruses

*Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements – Ellina Trofimova and Paul R Jaschke – bioRxiv

The gut virome of healthy children during the first year of life is diverse and dynamic – Blanca Taboada – PlosOne


Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Research

*Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox – Jakob Wirbel – Genome Biology

Review: Integrating pan-genome with metagenome for microbial community profiling – Chaofang Zhong – Computational and Structural Biotechnology Journal

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing – Caitlin M. Singleton – Nature Communications

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles – Christopher Gaulke – bioRxiv

Democratising deep learning for microscopy with ZeroCostDL4Mic – Lucas von Chamier – Nature Communications


Offered talks on Plasmids and Mobile Elements for 2021 – Plasmids around the globe – International Society for Plasmid Biology and Other Mobile Genetic Elements

Spring 2021 Microbiome Informatics webinars – OSU Center of Microbiome Science

EMBARK Spring Webinars – AMR focused webinars – EMBARK project

BISMiS Live – Microbial taxonomy: where are we now and where are we going? Iain Sutcliffe – Bergey’s Intl. Society for Microbial Systematics; registration here

Berkeley Lab Live Science – Exploring Earth – Berkeley Lab – April 23


ISAPP 2021 Virtual Annual Meeting – International Scientific Association for Probiotics and Prebiotics – June 1–2


Open Online R Stream – Wolfgang Viechtbauer

RaukR: Advanced R for Bioinformatics Summer School – NBIS/SciLifeLab – June 14-24

April 14, 2021

General microbiome

[REVIEW]The microbiome and human cancer – Sepich-Poore et al. – Science

[PERSPECTIVE]A framework for microbiome science in public health – Wilkinson et al. – Nature Medicine

A framework for microbiome science in public health –

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – Science Advances

Human gut microbiome

[REVIEW]Immune System, Microbiota, and Microbial Metabolites: The Unresolved Triad in Colorectal Cancer Microenvironment – Hanus et al. – Front. Immunol.

[REVIEW]Microbiome and colorectal cancer: A review of the past, present, and future – Johns & Petrelli – Surgical Oncology

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

Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition – Colombo et al. – eLife

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns – Juanola et al.

Animal microbiome (for animals in the wild)

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis – Dittmer & Brucker – Microbiome

Plant, root, and soil microbiome

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation – Li et al. – Microbiome

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils – Bao et al. – Microbiome

Rhizosphere community selection reveals bacteria associated with reduced root disease – Yin et al. – Microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Perez-Mon – Microbioal Genomics

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

[PREPRINT]The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean – Wietz et al. – bioRxiv

Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities – Fortunato et al. – Environmental Microbiology


[PREPRINT]Plasmid fitness costs are caused by specific genetic conflicts – Hall et al. – bioRxiv


[PREPRINT]Comprehensive benchmarking of tools to identify phages in metagenomic shotgun sequencing data – Ho, Millard & van Schaik – bioRxiv