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

December 7, 2020

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


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

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

General Microbiome

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

Gut microbiome

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

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

Human respiratory microbiome

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

Animal microbiome

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

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


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

Non-microbiome pick 

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

November 27, 2020

Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv


Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives


Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 14, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find great papers, in particular in soil and water microbiology but also in bioinformatics! As an example, Mara and collaborators are exploring the viruses found in the oxygen-deficient water column of the Cariaco basin. Interestingly, a large diversity of viral Auxilliary Metabolic Genes (AMGs) were found and give new insights in how phages may interact with their bacterial hosts in this understudied ecosystem.

In the bioinformatics section, I recommend anyone interested in phage metagenomics to take a look at the paper from Ren and collaborators. The authors have developed a reference-free and alignment-free deep learning tool, called DeepVirFinder, allowing the retrieval of viral sequences in metagenomes.

Today’s non-microbiology digest is a paper announcing the last update of the Genome Online Database (GOLD), a manually curated collection of genome projects and their metadata from around the world, which now contains more than a million entries! Great news for bioinformaticians!

Have a great Saturday!

Human gut microbiome

The bacterial association with oral cavity and intra-abdominal abscess after gastrectomy – Nishikawa et al. – PlosOne

Animal microbiome

Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians – Kishimoto et al. – ISME Journal

Plant, root, and soil microbiome

A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases – Tian et al. – ISME Journal

Air microbiome

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait – Al Salameen et al. – PlosOne

Water and extremophile microbiome

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system – Huber et al. – ISME Journal

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities – Kraemer et al. – ISME Journal

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline – Mara et al. – ISME Journal

Phages and Viruses

Metagenomic Analysis of the Enteric RNA Virome ofInfants from the Oukasie Clinic, North West Province,South Africa, Reveals Diverse Eukaryotic Viruses – Mogotsi et al. – Viruses


Identifying viruses from metagenomic data using deep learning – Ren et al. – Quantitative Biology

Review: Reconstructing organisms in silico: genome-scale models and their emerging applications – Fang et al. – Nature Reviews Microbiology

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data – Zhang et al. – PlosOne

Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach – Kirzhner et al. – PlosOne

Survey of metaproteomics software tools for functional microbiome analysis – Sajulga et al. – PlosOne


Sample pooling methods for efficient pathogen screening: Practical implications – Furstenau et al. – PlosOne

My non-microbiology picks

Genomes OnLine Database (GOLD) v.8: overview and updates – Mukherjee et al. – Nucleic Acids Research

September 10, 2020

Good morning from smokey, apocalyptic San Francisco! The world outside my window may be in sepia tones, but the articles I’m highlighting here are helping to brighten my day. Today’s digest has some fascinating insect and environmental microbiome research including a paper about the gut microbiota of a beetle that lives in the mixed forest of northeastern Asia and its capacity to efficiently degrade polystyrene. Additionally, there’s a paper characterizing the community structure and metabolic capacity of a biofilm-like microbial community lining the wall of the Yumugi river cave in a remote part of Western New Guinea. I’ve also included a paper examining availability of microbial community sequencing data which found that much of this data is not available and offers suggestions for improving data archiving practices. Finally, there is a very interesting technique paper about an orally ingestible microdevice that can be used to sample the gut microbiota in the upper gastrointestinal tract. Happy reading!

General Microbiome
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. – Ma, J. et al., Cancers

Experimental (co)evolution in a multi-species microbial community results in local maladaptation. – Castledine, M. et al., Ecology Letters

Pregnancy and Early Life
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. – Asbury, M.R et al., Cell Host Microbe

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. – He, Q. et al., Gut Microbes

Skin microbiome
Stratum Corneum Lipidomics Analysis Reveals Altered Ceramide Profile in Atopic Dermatitis Patients Across Body Sites With Correlated Changes in Skin Microbiome. – Emmert, H. et al., Experimental Dermatology

Vaginal microbiome
Diverse vaginal microbiome was associated with pro-inflammatory vaginal milieu among pregnant women in Uganda. – Bayigga, L. et al. Human Microbiome Journal

Gut microbiome
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. – Tuganbeav, T. et al., Cell

Microbiota-modulated CART + enteric neurons autonomously regulate blood glucose. – Muller, P.A. et al., Science

Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. -Banerjee, A. et al., Gastroenterology

Animal Experiments
Gut microbiome improves postoperative cognitive function by decreasing permeability of the blood-brain barrier in aged mice. – Wen, J. et al., Brain Research Bulletin

Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress. – Sári, Z. et al., Cancers

Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. – Sun, D. et al., Gut

Gut Microbiota-Associated Activation of TLR5 Induces Apolipoprotein A1 Production in the Liver. – Yiu, J.H.C. et al., Circulation Research

Animal and insect microbiome
Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. – Luter, H.M. et al., Environmental Microbiology

Symbionts shape host innate immunity in honeybees. – Horak, R.D. et al., Proceedings Biological Sciences

Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly. – Nguyen, B. et al. Microorganisms

Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. – Woo, S. et al., Applied and Environmental Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks. – Wang, K. et al., Journal of Hazardous Materials

Plant, root, and soil microbiome
Characteristics of microbial community of soil subjected to industrial production of antibiotics. – Borčinová, M. et al., Folia Microbiologica

Host selection shapes crop microbiome assembly and network complexity. -Xiong, C. et al., The New Phytologist

Microbiome of root vegetables-a source of gluten-degrading bacteria. – Kõiv, V. et al., Applied Microbiology and Biotechnology

Water and extremophile microbiome
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. – Wang, Z. et al., ISME Journal

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. – Xue, C-X et al., Microorganisms

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea. – Turrini, P. et al., Microbiological Research

Built environment
Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city-scale in Hong Kong across seasons. – Zhou, Y. et al., Environmental Science and Technology

Phages and viruses
Review: Phages and their potential to modulate the microbiome and immunity. Federici, S. et al., Cellular and Molecular Immunology

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures. – Chen, B. and Xu, W., PLoS Computational Biology

The Nubeam reference-free approach to analyze metagenomic sequencing reads. – Dai, H. and Guan, Y., Genome Research

The archives are half-empty: an assessment of the availability of microbial community sequencing data. – Jurburg, S.D. et al., Communications Biology

An effective culturomics approach to study the gut microbiota of mammals. – Pereira, A.C. and Cunha, M.V., Research in Microbiology

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. – Reichart, N.J. et al., ISME Journal

An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers. – Chen, L. et al., ACS Nano

August 10th, 2020

God morgon!

Good morning from Sweden. Today’s digest is a light one but carries a preprint with some very important findings. The study has suggested that the nCoV can potentially hijack the immune system completely by infecting the lymphocytes. This might lead to impaired antibody and T-cell response, something that could have a serious implication on the success of the much-awaited vaccine. (Unfortunately, for some unknown reasons, the PDF of the preprint is inaccessible to me! Let me know down in the comments if you are able to download it.)

A new paper in BMC microbiome shows a correlation between the indoor dust microbiota and the microbiota of infant airways. A classic example of how our environment impacts our health.  There is another interesting preprint where the authors show that a fungus alters its virulence when it is challenged by predatory amoebae. Perhaps the amoeba challenge selects for the warrior mutants which then carry on their warring ways!

Elsewhere in the digest is a preprint where Plasmodium knowlesi was used as a model to successfully determine new vaccine targets against more dangerous Plasmodium vivax, a paper detailing the effect of polar light cycles on the Antarctic lake microbiome, and identification of haloarchael species in Korean gut microbiota.


Preprint: Infection of human lymphomononuclear cells by SARS-CoV-2 – Marjorie C Pontelli, et al.

General Microbiology

Preprint: Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence – Man Shun Fu, et al.

Preprint: Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates – Duncan N Ndegwa, et al.

General microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar, et al. – Microbiome

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota – Shashank Gupta, et al. – Microbiome

Archaea/Gut microbiota

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Joon Yong Kim, et al. – Microbiome


Preprint: Successful introduction of the Colour Test into inexperienced settings – Kadri Klaos

Zoom Seminar

How a healthy gut microbe affects your whole body? – Karen Ranzi, Holistic Health Coach, Award-Winning Author, Motivational Speaker, Natural Foods Chef, Speech and Feeding Therapist (phew!)

August 4, 2020

Greetings Everyone. Today’s Microbiome Digest comprises of a wide variety of topics covering soil microbiota, tumor to water to extremophile microbiome. The digest has some reviews, books, as well as interesting articles on how synthetic microbial communities facilitate sustainable growth and the role of microbial communities in balancing the environment. A terrific news article covering the isolation of microbes buried beneath the sea floor for more than 100 million years. Today’s digest can be summarized by a quote by Julie Morley.

“Every being devotes and dedicates itself to some innate purpose. Single cells, microbes, plants, insects, animals – every being makes it own unique contribution” – Julie J. Morley

General microbiome

*Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae) – Jonas Frankel-Bricker – Scientific Reports

Microbiome-derived metabolites reproduce the mitochondrial dysfunction and decreased insulin sensitivity observed in type 2 diabetes – Ormsby et al – bioRxiv

*Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth – Zuñiga et al – Nature Communications

Multi-site human microbiome

Microbiome harbored within tumors: a new chance to revisit our understanding of cancer pathogenesis and treatment – Zhao et al – Signal Transduction and Targeted Therapy

Human skin microbiome
Paradigms and Perspectives: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al – The journal of Allergy and Clinical Immunology

Human gut microbiome
Review: Gut microbiota and atherosclerosis: role of B cell for atherosclerosis focusing on the gut-immune-B2 cell axis – Chen et al – Journal of Molecular Medicine

Gut microbiome a promising target for management of respiratory diseases – Trivedi et al – Biochemical Journal

*A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota – Aakko et al – Scientific Reports

Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health – Ribeiro et al – ACS Infect. Dis

Animal experiments
Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis – Pascottini et al – Scientific Reports

Plant, root, and soil microbiome
Book chapter: The Extended Microbiota: How Microbes Shape Plant-Insect Interactions – Mayoral-Peña et al – Evolutionary Ecology of Plant-Herbivore Interaction

Response of Soil Microbial Community to C:N:P Stoichiometry along a Caragana korshinskii Restoration Gradient on the Loess Plateau, China – Zhang et al – forests

Review: The endosphere microbial communities, a great promise in agriculture – Adeleke et al – International Microbiology

Water and extremophile microbiome
Influence of microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica – Krauze et al – Biogeosciences

Review: Microbial communities of soda lakes and pans in the Carpathian Basin: a review – Tamás Felföldi – Biologia Futura

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island) – dos Santos et al – microorganims

Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment – Ali et al – Geomicrobiology Journal

Review: Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis – James G. Ferry – Front.Microbiol

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation – Chung et al – Front.Microbiol

Food microbiology
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation – Vaccalluzzo et al – Food Microbiology

Book: A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria – Seena et al – Methods to Study Litter Decomposition

Review: Method development for cross-study microbiome data mining: challenges and opportunities – Su et al – Computational and Structural Biotechnology Journal

Microbes in the news
*Scientists pull living microbes, possibly 100 million years old, from beneath the sea – Elizabeth Pennnisi – Science

July 1, 2020

Greetings Everyone,
I want to began the month of July on a note that diversity is the basis for life. I can’t think of anything better to teach us about diversity, co-existence, and evolution than the fascinating Microbiome.
The microbiome affects us right from our birth till the end affecting our mental as well as physical health. The microbiome exhibits all sorts of differences in shape, size, color, metabolic functions in order to sustain life.
Much to learn from these tiny beings!!!!
Today’s Digest comprises of some interesting studies about effect of microbiome on chemotherapy and studies on tumor microbiome. It also includes articles exploring genetics of gut microbiome and the role of microbiome in inflammatory bowel disease. Additionally has a news article about taking microbiome therapies to clinical trials.
Hope you enjoy reading today’s digest!!
“Life on earth is such a good story you cannot afford to miss the beginning… Beneath our superficial differences we are all of us walking communities of bacteria. The world shimmers, a pointillist landscape made of tiny living beings”. – Lynn Margulis

General microbiome
Human Microbiota and Effectiveness of Cancer Chemotherapy – Shvets et al – Experimental Oncology

Immunity to commensal skin fungi promotes psoriasiform skin inflammation – Hurabielle et al – PNAS

Human Tumor microbiome
*Perspective: Probing the tumor micro(b)environment – Atreya et al – Science

Human Eye microbiome
Review: Current Knowledge on the Human Eye Microbiome: A Systematic Review of Available Amplicon and Metagenomic Sequencing Data – Delbeke et al – Acta Ophthalmologica

Human nearly-sterile sites (blood, organs, brain)
Blood Bacterial Profiles Associated with HIV Infection and Immune Recovery – Serranno-Villar et al – The Journal of Infectious Diseases

Human gut microbiome
*Genetics of human gut microbiome composition – Kurilshikov et al – bioRxiv

Review: The microbiome in inflammatory bowel diseases: from pathogenesis to therapy – Liu et al – Protein&Cell

Built environment
Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al – bioRxiv

Food microbiology
Food and mood: how do diet and nutrition affect mental wellbeing? – Firth et al – BMJ

DRAM for distilling microbial metabolism to automate the curation of microbiome function – Shaffer et al – bioRxiv

MetaRibo-Seq measures translation in microbiomes – Fremin et al – Nature Communications

Microbes on the market
Enterome Secures €46M to Take Microbiome Therapies to Clinical Trials – Helen Albert –

Human Microbiome Therapeutics Market Research: Global Status & Forecast by Geography, Type & Application (2016-2026)

May 22, 2020

We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!


Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv


Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases


Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome


Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

March 5, 2020

Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.


Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth – Elena Zagato et al. – Nature Microbiology

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports


Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li et al. – Science of the Total Environment

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere


Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research


Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome –

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature