April 2, 2021

Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water


***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems

March 28th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in marine microbiology and virology, I recommend taking a look at the paper by Gazitúa and collaborators. In this study they investigated the role of phages in shaping the metabolism metabolic networks along redox gradients associated with marine oxygen minimum zones. To do so, they investigated the phage contents in auxiliary metabolic genes involved in bacterial photosynthesis, central carbon metabolism, and nutrient cycling.  

Today’s non-microbiology pick is a web-platform, called Sysrev, built to aid in systematic evidence reviews. Sysrev contains thousands of Findable, Accessible, Iteroperable and Reusable (FAIR) datasets from a large variety of disciplines.

Have a great Sunday!

Human gut microbiome

Preprint: Fecal microbiome of children with norovirus gastroenteritis – Merces Hernandez et al. – bioRxiv 

Plant, root, and soil microbiome

Preprint: Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands – Wang et al. – bioRxiv 

Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. – Bernard et al. – ISME J

Distribution patterns of Acidobacteriota in different fynbos soils – Conradie and Jacobs – PLOS

Water and extremophile microbiome

Preprint: Epidemiological dynamics of viral infection in a marine pico-eukaryote – Listmann et al. – bioRxiv  

Preprint: A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation – Liu et al. – bioRxiv

Preprint: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments – Ting-Shyang Wei et al. – bioRxiv  

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community – Seyler et al. – ISME J

Food microbiology

Preprint: Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance – Stanford et al. – bioRxiv

Phages and viruses

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters – Gazitúa et al. – ISME J


Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Shion et al. – bioRxiv

My non-microbiology picks

Preprint: Sysrev: A FAIR Platform For Data Curation And Systematic Evidence Review – Bozada et al. – bioRxiv

March 18, 2021

Greetings from Pittsburgh!

Today’s digest has a lot of food and agriculture associated articles. Several articles focus on the effects of various pathogens on dairy cows, beef steers, and poultry breeds! For those of us who are more interested in plants, there is an article on biogas production from tomato waste and a preprint on how the microbial community of food waste changes during the composting process. Finally, I included a research article about social media during the pandemic since I’m sure I’m not the only one who has relied on it a little too heavily over the last year…

Happy reading!

General microbiome

Preprint: Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations – Conrad et al. – bioRxiv

BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE – Demo et al. – PLOS ONE

Review: The gut microbiota–brain axis in behaviour and brain disorders – Morais et al. – Nature Reviews Microbiology

Preprint: Cross-species evolutionary rewiring in the enteric bacterium Campylobacter – Taylor et al. – bioRxiv

Human gut microbiome

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis – Vega et al. – PLOS ONE

Animal experiments

Preprint: Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines – Chrzastek et al. – bioRxiv

Preprint: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks – Hamilton et al. – bioRxiv

Animal microbiome

Preprint: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe – Wallace et al. – bioRxiv

Plant, root, and soil microbiome

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe – Jia et al. – PLOS ONE

Preprint: Changes and composition of microbial community during aerobic composting of household food waste – Jin et al. – bioRxiv

Preprint: What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits – Steven et al. – bioRxiv

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems – Szilágyi et al. – PLOS ONE

Food microbiology

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers – Roque et al. – PLOS ONE

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania – Thomas et al. – PLOS ONE

Multidrug-resistant enterobacteria in newborn dairy calves in Germany – Waade et al. – PLOS ONE

Phages and viruses

Review: Viral and host heterogeneity and their effects on the viral life cycle – Jones et al. – Nature Review Microbiology


Dcmd: Distance-based classification using mixture distributions on microbiome data – Shestopaloff et al. – PLOS Computational Biology

Kara’s non-microbiology pick

Don’t put all social network sites in one basket: Facebook, Instagram, Twitter, TikTok, and their relations with well-being during the COVID-19 pandemic – Masciantonio et al. – PLOS ONE

February 27th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in gut microbiomes, I recomment taking a look at the preprint by Weiss and collaborator. In this study, they explore bacteria-bacteria interactions, bacterial growth and metabolic interactions in a synthetic bacterial community: the Oligo-Mouse-Microbiota, which is increasingly used as model system in gut microbiome research.

Additionally, anyone interested in microbiome-based forensic tools should read the study from Sang You and collaborators.  They compared the composition of microbial communities in blood spot surfaces placed in different environments sampled across seasons and time points, in order to evaluate the environmental factors leading to variation in these microbial communities.

Today’s non-microbiology pick is a fascinating study looking at the prevalence of COVID-19 related misinformation among the Yemeni population and its association with vaccine acceptance and perceptions. From this study, the authors recommend the deployment of awareness campaigns to decrease misinformation before initiating any mass vaccination in Yemen.

Have a great Weekend!

Human gut microbiome

Review: The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling – Gangadoo et al. – International Journal of Molecular Sciences

Preprint: Exploring the interaction network of a synthetic gut bacterial community – Weiss et al. – BioRxiV

Animal experiments

Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions – Rehman Kayani et al. – Environmental Pollution

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea – Jo et al. – Environmental Pollution

Influence of environmental factors and bacterial community diversity in pond water on health of Chinese perch through Gut Microbiota change – Li et al. – Aquaculture Reports

Preprint: The diversity, composition, and metabolic pathways of archaea in pigs – Deng et al. – Preprints

Animal microbiome

Preprint: Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach – Becker et al. – bioRxiV

Built environment

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Sang You et al – FEMS Microbiology letters

Phages and viruses

Opinion paper: Rapid emergence of virus–host mutualism under stress – Dolja – PNAS

Patterns of virus growth across the diversity of life – Jin and Yin – Integrative biology


Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity – Carroll-Portillo et al. – Viruses

My non-microbiology picks

Preprint: Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen – Naoras Bitar et al. – BioRxiV

February 4, 2021

Greetings from a very snowy Pittsburgh!

If you like getting dirty, today’s digest is for you! It includes a review on bat guano, two research articles about compost, four focused on soil research, and a preprint about fertilization with poultry manure.

Happy reading!

Events and jobs

February 1st to 14th: If you’re on twitter, check out #MicrobeValentinesDay! @AnneAMadden is posting 14 days of pink microbes in honor of Valentine’s Day under this hashtag!

Human skin microbiome

Gut microbiome profile in psoriatic patients treated and untreated with biologic therapy – Valentini et al. – The Journal of Dermatology

Human gut microbiome

Preprint – Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement – Barrasso et al. – bioRxiv

Review: Gut microbiota-mediated pesticide toxicity in humans: methodological issues and challenges in risk assessment of pesticides – Utembe and Kamng’ona – Chemosphere

Animal experiments

Effects of thallium exposure on intestinal microbial community and organ functions in zebrafish (Danio rerio) – Wang et al. – Elementa: Science of the Anthropocene

Is intestinal bacterial diversity enhanced by trans-species spread in the mixed-species flock of hooded crane (Grus monacha) and bean goose (Anser fabalis) wintering in the lower and middle Yangtze river floodplain? – Yang and Zhou – Animals

Animal microbiome

Review: The microbiome of bat guano: for what is this knowledge important? – Dimkić et al. – Applied Microbiology and Biotechnology

Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source – Kueneman et al. – Microbial Ecology

Plant, root, and soil microbiome

Survival rates of microbial communities from livestock waste to soils: a comparison between compost and digestate – Akari and Uchida – Applied and Environmental Soil Science

Year, location, and variety impact on grape-, soil-, and leaf-associated fungal microbiota of Arkansas-grown table grapes – Cureau et al. – Microbial Ecology

Preprint: Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile – Frentrup et al. – bioRxiv

Impacts of invasive Australian Acacias on soil bacterial community composition, microbial enzymatic activities, and nutrient availability in Fynbos soils – Keet et al. – Microbial Ecology

A novel carboxylesterase derived from a compost metagenome exhibiting high stability and activity towards high salinity – Lu and Daniel – Genes

A two-year field study of nickel-agromining using Odontarrhena chalcidica co-cropped with a legume on an ultramafic soil: temporal variation in plant biomass, nickel yields and taxonomic and bacterial functional diversity – Saad et al. – Plant and Soil

Bacterial response to soil property changes caused by wood ash from wildfire in forest soils around mining areas: Relevance of bacterial community composition, carbon and nitrogen cycling – Zhang et al. – Journal of Hazardous Materials

Water and extremophile microbiome

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu – Chen et al. – Science of the Total Environment

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs – He et al. – Science of the Total Environment

Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep‐sea bacterium Pseudoalteromonas sp. MT33b – Ma and Sun – Environmental Microbiology Reports

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Built environment

Preprint: Half-life of biodegradable plastics in the marine environment depends on material, habitat, and climate zone – Lott et al. – bioRxiv

Water flushing irremovable biofilms on support material in dynamic membrane bioreactor: formation, composition, and microbial community – Huang et al. – Chemosphere

Phages and viruses

Preprint: Rampant prophage movement among transient competitors drives rapid adaptation during infection – Marshall et al. – bioRxiv

January 24, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in  early-life microbiome, I recommend taking a look at the paper from Mortensen and collaborators. To understand the role of the maternal vaginal microbiome’s in seeding their child and the importance of the delivery mode in early-life microbiome acquisition, they studied 665 mother–child dyads and modeled the transfer of the vaginal microbiota from mother to infants.

In today’s digest, you’ll also find a really interesting preprint from Abiriga and collaborators, looking at the microbiome of a groundwater aquifer contaminated by a municipal landfill while undergoing intrinsic bioremediation. This preprint is particularly notable because studies looking at the microbiome of contaminated aquifers are particularly rare, despite groundwater contaminations from landfills being a very common issue.

Today’s non-microbiology pick takes a look at the difficulty of detecting scientificly fraudulent images produced by Generative Adversarial Networks (GANs). They demonstrate that this deep-learning method can generate realistic western blot images that are indistinguishable from real western blots. In conclusion, the authors argues that additional information should be required to ensure that the western blots published in scientific publication are not generated images. 

Have a great Sunday!

Human respiratory microbiome

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism – Sulaiman et al. – European respiratory journal

Human skin microbiome

Preprint: Comparative investigation of the Diabetic foot ulcer microbiome – Saeb et al. – BioRxiv

Human vaginal microbiome

Preprint: Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control – Goodfellow et al. – MedRxiv

Modeling transfer of vaginal microbiota from mother to infant in early life – Mortensen et al. – eLife

Human gut microbiome

Review: Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations – Lamichhane et al. – Metabolites

Animal microbiome

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus) – Funosas et al. – Scientific reports

Plant, root, and soil microbiome

Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic – Varsadiya et al. – FEMS Microbial ecology

Book chapter: Microbial Diversity of Phyllosphere – Dhankhar et al. – Phytomicrobiome Interactions and Sustainable Agriculture

Review: Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome – Singer et al. – Phytomes journal

Water and extremophile microbiome

Book chapter: Potential of Extremophiles for Bioremediation – Kaushik et al. – Microbial Rejuvenation of Polluted Environment. Microorganisms for Sustainability, vol 25. Springer, Singapore.

Built environment

Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing – Lee et al. – Microbiology ressource announcements

Preprint: Characterisation of the bacterial microbiota of a landfill-contaminated confined aquifer undergoing intrinsic remediation – Abiriga et al. – BioRxiv

Phages and viruses

Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child – Manohar et al. – Human Microbiome Journal

Review: Enteric Viruses and Inflammatory Bowel Disease – Tarris et al. – Viruses


book chapter: Advances in Omics and Bioinformatics Tools for Phyllosphere Studies – Bansal – Phytomicrobiome Interactions and Sustainable Agriculture

MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning – Dhungel et al. – BMC Bioinformatics

My non-microbiology picks

Preprint: Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation – Qi et al. – BioRxiv

January 14, 2021

Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.

General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International

December 18, 2020

Greetings from cold and snowy Pittsburgh!

As I type this, my housemate (who is an essential healthcare worker) should be getting the first dose of her COVID-19 vaccine! Although I’m not sure what the distribution of COVID-19 vaccines is expected to look like, today’s digest includes an article mapping routine measles vaccination coverage in low- and middle- income countries. I’ve also highlighted a few interesting environmental microbiology preprints, including one on the role of ecosystem engineers in shaping arid soil bacterial communities.

Happy holidays and happy reading!

Events and jobs

Danone North America Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Applications for the 2020-2021 grant are currently open and are due on February 24, 2021.

General microbiome

Mapping routine measles vaccination in low- and middle-income countries – Local Burden of Disease Vaccine Coverage Collaborators – Nature

The functional proteome landscape of Escherichia coli – Mateus et al. – Nature

Preprint: Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities – Baubin et al. – bioRxiv

Preprint: Environmental interactions with amoebae as drivers of bacterial-fungal endosymbiosis and pathogenicity – Itabangi et al. – bioRxiv

November 26, 2020

Greetings from Pittsburgh!

Today’s digest is heavy on environmental microbiology work, especially plant, root, and soil microbiome studies. I also want to highlight a fun research paper (and paired Wired article) on the microbiome of da Vinci’s drawings.

Happy reading! And for all of those in the U.S. who are celebrating the Thanksgiving holiday, please be safe and follow all local COVID precautions.

Multi-site human microbiome

Mycobiome changes in the vitreous of post fever retinitis patients – Arunasri et al. – PLOS ONE

Review: Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases – Konjevod et al. – Journal of Pharmaceutical and Biomedical Analysis

Animal experiments

Cerumen microbial community shifts between healthy and otitis affected dogs – Borriello et al. – PLOS ONE

Plant, root, and soil microbiome

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types – Evdokimova et al. – PLOS ONE

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata – Ihua et al. – PLOS ONE

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere – Zhao et al. – PLOS ONE

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale – Zhuang et al. – npj Biofilms and Microbiomes

Water and extremophile microbiome

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient – Euler et al. – PLOS ONE

Built environment

**The microbiome of Leonardo da Vinci’s drawings: A bio-archive of their history – Piñar et al. – Frontiers in Microbiology

Microbes in the news

**Meet the microbes living on Da Vinci’s iconic sketches – Simon – Wired

Science, publishing, and career

Postdocs under pressure: ‘Can I even do this any more?’ – Woolston – Nature

November 20, 2020

Today’s digest features a systematic assessment of best practices for the sequencing-based characterization of the human vaginal microbiome, studies on link between the plaque microbiome and peri-implantitis, cutimycin [a Cutibacterium acnes-produced antibiotic that affects niche competition among the human skin microbiota] and antibiotic resistance genes in shower drains, washing machines, and dishwashers. There is a new Micro Binfie Podcast episode about moving from the wet lab into the dry lab to become a bioinformatician. Also, check out a list of interesting (freely available) events. Happy reading/listening!

Oral microbiome

*Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics – Paolo Ghensi – npj Biofilms and Microbiomes

Skin microbiome

*A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles – Jan Claesen – Science Translational Medicine

Review: Staphylococcus epidermidis—Skin friend or foe? – Morgan M. Brown and Alexander R. Horswill – Plos Pathogen

Gut microbiome

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts – Stephen A. James – Journal of Fungi

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology – Antonio Molinaro – Nature Communications

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Allyson L. Byrd – Journal of experimental medicine

Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements – Rupasri Mandal – Metabolomics

Minireview: Communal Living: Glycan Utilization by the Human Gut Microbiota – Jonathon A. Briggs – Environmental Microbiology

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut – Leszek Michalak – Nature Communications

Vaginal microbiome

*Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome – Luisa W. Hugerth – mSphere

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily – npj Biofilms and Microbiomes

Intercepting genomic variability of Gardnerella vaginalis species through comparative genomics analyses: evolutionary and ecological implications – Chiara Tarracchini – Applied and Environmental Microbiology

Engineered phage endolysin eliminates Gardnerella in bacterial vaginosis without damaging the healthy vaginal microbiome – Christine Landlinger – medRxiv

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Katelyn Brandt & Rodolphe Barrangou – BMC Microbiology

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Wendy Li and Zhanshan Sam Ma – Computational and Structural Biotechnology Journal

Animal microbiome

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens – Simon Daniels – Plos One

Review: Value of Probiotics in Canine and Feline Gastroenterology – Silke Salavati Schmitz – Veterinary Clinics of North America: Small Animal Practice

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel – Marco Gerdol – Genome Biology


Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach – Shaktheeshwari Silvaraju – Applied and Environmental Microbiology


Metagenomic assessment of the global distribution of bacteria and fungi – Mohammad Bahram – Environmental Microbiology


On the complexity of haplotyping a microbial community – Samuel M Nicholls – Bioinformatics

Challenges in Benchmarking Metagenomic Profilers – Zheng Sun – bioRxiv

Unifying the global coding sequence space enables the study of genes with unknown function across biomes – Chiara Vanni – bioRxiv

Nucleotide-resolution bacterial pan-genomics with reference graphs – Rachel M Colquhoun – bioRxiv

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools – Hao Hou – bioRxiv

An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome – Nicolas Nalpas – bioRxiv

The misuse of colour in science communication – Fabio Crameri – Nature Communications

Antimicrobial Resistance

*The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering – Laura Schages – Applied and Environmental Microbiology

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm – Shireen M Kotay – bioRxiv

fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota – Sami Khabthani – Antimicrobial Agents and Chemotherapy

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile – Ilse M. Boekhoud – bioRxiv


Black In Immuno WeekBlack in Immuno – 22-28 November 2020
*A collective of scientists to celebrating, amplifying, and promoting the work of Black Immunologists across the globe.

Webinar: Antibiotic Resistance in the Environment – Organizer: Resistomap – Date: Tuesday, 24 November 2020

Webinar: Microbiology Webinars – FEMS – webinar recordings available

Virtual course and symposium: Harnessing Our Inner Ecology To Track and Treat Disease – Institute for Systems Biology – October 15 and 16, 2020
*all course materials/tutorials and talks are available for free on the website

Virtual Conference on Prokaryotic Small Proteins – Organizers: Todd Gray, Kai Papenfort, Gigi Storz and Joe Wade – January 12-14, 2021


*Moving from wet to dry with Phil Ashton – Hosts: Andrew Page, Nabil-Fareed Alikhan and Lee Katz – Micro Binfie Podcast

Real-time quantitative proteomics with Devin Schweppe – Host: Jacob Schreiber – The Bioinformatics Chat

Interspecies collaborations with Mindaugas Gapševičius – Host: Aga Pokrywka – Ferment Radio

Microbiome as Organ: Researcher Colin Hill Talks Bacteria and Bacteriophages in Human Body with Colin Hill – Host: Richard Jacobs – The Finding Genius Podcast

What Does Your Microbiome Say About You? with Colin Hill – Host: Andrea Hardy – Let’s Gut Real

Colouring booklet

Microbes, diet and beyond by Microbiome Support EU project; Illustrations by Maria Pock


Drugs vs Bugs, a free and exciting Print’n’Play boardgame developed by Célia Souque