May 28, 2020

Hello and welcome to today’s microbiome digest! It’s a compact digest, but quite diverse. You will find a study investigating the effect of high-fat diet in Drosophila found a microbiota-dependent activation of stem-cells; electronic cigarettes were found to negatively influence the oral microbiome, and glycan epitopes present on enveloped viruses (as COVID-19) can be targeted and neutralized by human antibodies against these foreign glycan structures.
Finally, a helpful article during Corona-times, when more and more courses and meetings are held online, features the use of FAIR training material: Ten simple rules for making training materials FAIR. Enjoy!


Is social connectedness a risk factor for the spreading of COVID-19 among older adults? The Italian paradox – Giuseppe Liotta – PLOS ONE

General microbiome

Review: Enhancing bacterial survival through phenotypic heterogeneity – Leila M. Reyes Ruiz – PLOS PATHOGENS

Human respiratory microbiome

Adverse effects of electronic cigarettes on the disease-naive oral microbiome – Sukirth M. Ganesan – Science Advances

Human gut microbiome

Preprint: Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss – Qi Wang – BioRxiv

Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma – Sean P. Polster – Nature Communications

Persistent Diarrhea in Patients With Crohn’s Disease After Mucosal Healing Is Associated With Lower Diversity of the Intestinal Microbiome and Increased Dysbiosis – Karen Boland – Clinical Gastroenterology and Hepatology

Fecal microbiota transplantation in systemic sclerosis: A double-blind, placebo-controlled randomized pilot trial – Havard Fretheim – PLOS ONE

Animal experiments

A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine – Jakob con Frieling – PLOS GENETICS

The cecal and fecal microbiomes and metabolomes of horses before and after metronidazole administration – Carolyn E. Arnold – PLOS ONE

Plant, root, and soil microbiome

Functional diversity of rhizosphere soil microbial communities in response to different tillage and crop residue retention in a double-cropping rice field – Haiming Tang – PLOS ONE

Water and extremophile microbiome

Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs – Lubov Chernogor – PeerJ

Built environment

The use of ozone gas for the inactivation of Bacillus anthracis and Bacillus subtilis spores on building materials – Joseph P. Wood – PLOS ONE

Phages and viruses

* Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 – Adrien Breiman – PLOS PATHOGENS

Review: A viral journey to the brain: Current considerations and future developments – Nilda Vanesa Ayala-Nunez – PLOS PATHOGENS


Preprint: A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence – Elisa Venturini – BioRxiv


Preprint: Fluorescent secreted bacterial effectors reveal an intravacuolar replication compartment for Listeria monocytogenes – Caroline Peron Cane – BioRxiv

Science, publishing, and career

2 Art Gallery Shows to Explore From Home – The New York Times – Check out the art by Anika Yi

Judith’s non-microbiology picks

* Ten simple rules for making training materials FAIR – Leyla Garcia – PLOS COMPUTATIONAL BIOLOGY

May 27, 2020

Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!

General microbiome

A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports

Multi-site human microbiome

REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research

REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.

Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand

Human oral microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports

Human skin microbiome

Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica

Human gut microbiome and virome

Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv

The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One

The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients

Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter

Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter

Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter

Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter


REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility

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

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology

Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Morck et al. – bioRxiv

Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition

Animal microbiome (for animals in the wild)

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal

Plant, root, and soil microbiome

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Zolti et al. – Microbiology

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

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc

Built environment (subways, indoor surfaces)

Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology

Food microbiology

Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients


ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research

Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications

May 19, 2020

Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!


Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al.Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al.European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al.Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al.Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al.PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al.Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al.Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al.BMC Microbiology


Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

May 9, 2020

Among the highlights for today, there’s an unusual preprint on using honeybees for proxy sampling of the urban microbiome, as well as a paper on the effect of captivity on the microbiome of raptors.

In some non-microbiome related news, the summarized highlights from the 5th International One Health Congress were recently published. Some of their recommendations regarding science and public health are particularly apt considering the present pandemic, and I found it to be quite an interesting read. You can find it here:

Make science evolve into a One Health approach to improve health and security: a white paper – Osterhaus et al. – One Health Outlook

I hope you’re all doing well, wherever you are!


Preprint: The coding capacity of SARS-CoV-2 – Finkel et al. – bioRxiv

Pregnancy and early life

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community – Koo et al. – Royal Society of Open Science

Animal microbiome

Preprint: Host evolutionary history and ecology shape virome composition in fishes – Geoghegan et al. – bioRxiv

The fecal microbiota of wild and captive raptors – Oliveira et al. – Animal Microbiome

Plant, root, and soil microbiome

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? – Kaplan et al. – Evolutionary Applications

Built environment

Preprint: Holobiont urbanism: sampling urban beehives reveals cities’ metagenomes – Henaff et al. – bioRxiv


Preprint: Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution – Matsuo et al. – bioRxiv

Quantifying technical confounders in microbiome studies – Bartolomaeus et al. – Cardiovascular Research

May 2nd, 2020

Another month has passed! Hope everyone is staying at home and being well. Today’s highlights include a paper applying NMR to monitor neonatal metabolic adaptations, how oil influence microbial community assembly off the Gulf of Mexico and a preprint for a Bayesian Multi-task method to identify global microbiome associations.

COVID-19 Articles 

Why the Coronavirus Is So Confusing – Ed Yong – The Atlantic

Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals – Liu & Ning et al. – Nature

Human microbiome

Fucosidases from the human gut symbiont Ruminococcus gnavus – Wu & Rebello et al– Cellular and Molecular Life Sciences

Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection – Grier et al. – bioRxiv **preprint**

Sex-specific Alterations in the Urinary and Tissue Microbiome in Therapy-naïve Urothelial Bladder Cancer Patients – Pederzoli et al.  – European Urology Oncology

Microbiome and Metabolomics 

Metabolic changes in early neonatal life: NMR analysis of the neonatal metabolic profile to monitor postnatal metabolic adaptations – Georgakopoulou, I., Chasapi, S.A., Bariamis, S.E. et al – Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling & Kostidis et al. – Nature Scientific Reports

Soil microbiome

Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils – Bi & Cai et al. – Chemosphere

Soil pH and C/N ratio determines spatial variations in soil microbial communities and enzymatic activities of the agricultural ecosystems in Northeast China: Jilin Province case – Xu et al. – Applied Soil Ecology

Animal microbiome

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer – Liu & Wang et al. – Virology Journal

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen & Cormican et al– PLOS One

Microbiomes of the built environment 

Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico – Noirungsee et al. – Nature Scientific Reports

Passenger-surface microbiome interactions in the subway of Mexico City – Vargas-Robles et al.  – bioRxiv **preprint**


Intra-species signaling between Pseudomonas aeruginosa genotypes increases production of quorum sensing controlled virulence factors – Mould et al. – bioRxiv **preprint**

Statistics and bioinformatics 

A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations – Hatami et al. – bioRxiv (soon to be published in Bioinformatics) **preprint**


Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant a-amylase – Deutch & Yang – Antonie van Leeuwenhoek

Aquatic environments  

Cyanobacteria in inland waters: new monitoring, reporting, modelling and ecological research – Mitrovic et al. – Marine & Freshwater Research **review**

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China – Tang et al. – Environmental Microbiome

Microbiome in the News

Coffee plants have a small but consistent core microbiome of fungi and bacteria – American Phytopathological Society – EurekAlert!

May 1, 2020

Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

April 26, 2020

Greetings from Pittsburgh, PA!

Today’s digest includes several reviews, numerous host-microbiome studies, a wide variety of environmental microbiome studies, and a new book focused on Emerging Technologies in Environmental Bioremediation.

I also wanted to highlight the virtual Fermentation Mini-Seminars offered by the Applied Ecology Department at my alma mater, NC State University. During the first seminar of the series I learned about the Wild Sourdough Project, which is a community-science/citizen-science project where participants can submit observational data about their sourdough culture. If you’re missing the lab, this might be the perfect project for you!

Virtual Events

NCSU Fermentation Mini-Seminars offered every Thursday at 4pm EST from April through August

General microbiome

Special Issue: Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals – De Vrieze et al. – Microbial Biotechnology

Review: Biofilm matrixome: Extracellular components in structured microbial communities – Karygianni et al. – Trends in Microbiology

Review: Microbial symbiosis: A network towards biomethanation – Saha et al. – Trends in Microbiology

Multi-site human microbiome

Microbiota in cerebrovascular disease: A key player and future therapeutic target – Tonomura et al. – Journal of Cerebral Blood Flow & Metabolism

Review: Role of microbiome and antibiotics in autoimmune diseases – Vangoitsenhoven and Cresci – Nutrition in Clinical Practice

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – BMC Microbiology

Human gut microbiome

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder – Dan et al. – Gut Microbes

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population – Koliada et al. – BMC Microbiology

Gut microbiome reveals specific dysbiosis in primary osteoporosis – Xu et al. – Frontiers in Cellular and Infection Microbiology

Animal experiments

The clinical drug Ebselen attenuates inflammation and promotes microbiome recovery in mice after antibiotic treatment for CDI – Garland et al. – Cell Reports Medicine

Effect of oxytetracycline treatment on the gastrointestinal microbiome of critically endangered white abalone (Haliotis sorenseni) treated for withering syndrome – Parker-Graham et al. – Aquaculture

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome – Rimoldi et al. – BMC Veterinary Research

Animal microbiome

(My microbiome) would walk 10,000 miles: Maintenance and turnover of microbial communities in introduced dung beetles – Parker et al. – Invertebrate Microbiology

Plant, root, and soil microbiome

Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil – Asem et al. – International Journal of Systemic and Evolutionary Microbiology

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.) – Das et al. – Scientific Reports

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland – Girkin et al. – Wetlands

Integrating transcriptomics and metabolomics to studies key metabolism, pathways and candidate genes associated with drought-tolerance in Carthamus tinctorius L. under drought stress – Wei et al. – Industrial Crops and Products

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China – Yang et al. – PeerJ

Water and extremophile microbiome

Impacts of an eruption on cold-seep microbial and faunal dynamics at a mud volcano – Girard et al. – Frontiers in Marine Science

Unraveling heterogeneity of coral microbiome assemblages in tropical and subtropical corals in the South China Sea – Gong et al. – Microorganisms

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances – Hou et al. – Water Research

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin – Nigro et al. – PLOS One

Near streambed flow shapes microbial guilds within and across trophic levels in fluvial biofilms – Risse-Buhl et al. – Limnology and Oceanography

Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading – Zhang et al. – Water Research

Built environment (subways, indoor surfaces)

Ecological processes affecting long-term eukaryote and prokaryote biofilm persistence in nitrogen removal from sewage – Angell et al. – Genes

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations – Kannan et al. – Bioresource Technology

Book: Emerging Technologies in Environmental Bioremediation – Edited by Shah et al.

Food microbiology

How processing methods affect the microbial community composition in a cereal-based fermented beverage – Phiri et al. – LWT – Food Science and Technology

High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu – Tang et al. – Frontiers in Microbiology