June 22, 2020

General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

June 21, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find two very interesting reviews! Stagaman and collaborators come back on years of Zebra-fish gut microbiome research and explore the insights gleaned from this awesome model animal. On the other hand, François and Pybus review our understanding of avian viromes in both wild and domesticated bird populations, highlighting the current limitations and pitfalls in this research area.

But today’s digest also contains very interesting research papers! Gulino and collaborators are exploring viromes in New York city wastewater systems. This paper is particularly interesting as bacteriophages are typically left out from urban environments microbiomes studies, despite their abundance and importance in ecosystems.

Finally, today’s non-microbiology pick is a review that comes back on how information theory, developped by Claude Shannon in the late 40s, have been used in computational biology. This paper is particularly interesting for readers wanting to learn more about the basics of information theory and how it is applied today in bioinformatics.

Have a great Sunday!

Pregnancy and early life

Review: The microbiome in pediatric oncology – Rotz et al. – Cancer

Human respiratory microbiome

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis – a pilot study – Hu et al. – Emerging Microbes & infections

Human vaginal microbiome

Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development –Nkufi Tange et al. – Scientific reports

Human gut microbiome

Preprint: The gut microbiome regulates memory function – Noble et al. – BioRxiV

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

review: Zebrafish microbiome studies make waves – Stagaman et al. – Lab Animal

Built environment (subways, indoor surfaces)

Revealing antimicrobial resistance in stormwater with MinION – Bialasek et al. – Chemosphere

Phages and viruses

Review: Towards an understanding of the avian virome –François et al. – Journal of general Virology

Initial Mapping of the New York City Wastewater Virome –Gulino et al. – mSystems


Higher order Markov models for metagenomic sequence classification – Burks et al. –Bioinformatics

Preprint: Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification –Zhu et al. –BioRxiV

Preprint: Ultra-rapid metagenotyping of the human gut microbiome – Shi et al. – BioRxiV

My non-microbiology pick

Review: Information Theory in Computational Biology: Where We Stand Today – Chanda et al. – Entropy

June 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

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 7, 2020

Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.

General microbiome

Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications

Human respiratory microbiome

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE

Human skin microbiome

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes

Human gut microbiome

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications

Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances

Animal experiments

Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv

Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology

Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology

Animal microbiome

Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B

Plant, root, and soil microbiome

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications

Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv

Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE

Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv

Water and extremophile microbiome

The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE

Built environment

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE


Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE

Phages and viruses

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE


Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE

Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE

April 23, 2020

The wave of new microbe enthausiasts keeps coming and with it a light digest for today.  I am writing to you from Bremen, Germany, with a selection including a wheat fungi that changes the wheat leaf microbiome and antimicrobial resistance genes identified by whole metagenome shotgun study of nasopharyngal colonization in South Africa.

There is also an interesting article about species identification errors occurring in context of large sequence collection platforms.
And to mix things up a little bit, at the end of a list you find a paper with amazing microscopy featuring the beautiful parasite Trypanosoma brucei and answering the endless question to how this parasite colonizes its insect host, the tsetse fly.

Human respiratory microbiome

Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing – Rendani I. Manenzhe – PLOS ONE

Human gut microbiome

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – PLOS BIOLOGY

Animal experiments

Preprint: Comparative analysis of beneficial effects of Vancomycin treatment on Th1- and Th2-biased mice and role of gut microbiota – Pratikshya Ray – bioRxiv

Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet – Simona Rimoldi – PLOS ONE

Lactobacillus reuteri attenuated allergic inflammation induced by HDM in the mouse and modulated gut microbes – Lingzhi Li – PLOS ONE

Animal microbiome

Occurrence of Mycoplasma gallisepticum in wild birds: A systematic review and meta-analysis – Anna Sawicka – PLOS ONE

Plant, root, and soil microbiome

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition – Heike Seybold – Nature Communications

Phages and viruses

SMOOT libraries and phage-induced directed evolution of Cas9 to engineer reduced off-target activity – Derek Cerchione – PLOS ONE


BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? – Mikko Pentisaari – PLOS ONE

Science, publishing, and career

A pedagogical approach to science outreach – Marni B. McClure – PLOS BIOLOGY

Judith’s non-microbiology picks

Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus – Clair Rose – Nature Microbiology

April 4, 2020

Good morning and salutations from Singapore! This is the first digest that I’m contributing for the blog, so I hope my selections are interesting to you all! Today’s digest begins with some recent COVID-19 pre-prints, before getting into papers on a diverse range of microbiome-related topics. Highlights today include a study on cats potentially harbouring SARS-CoV-2 (nooo…), the effect of C-section birth on the vaginal microbiota of adult women, and the impact of the virome on biogeochemical cycling in Lake Baikal.


Preprint: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia – Pizzorno et al.

* Preprint: SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation – Zhang et al.

Preprint: Direct RNA sequencing and early evolution of SARS-CoV-2 – Taiaroa et al.

General microbiome

Review: Microbiota and metabolites in rheumatic diseases – Tong et al. – Autoimmunity Reviews

Human respiratory microbiome

Preprint: Distinctive airway microbial ecology of smokers and asthmatics – Turek et al.

Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort – Bouquet et al.Respiratory Research

Human gut microbiome

An in vitro evaluation of the effects of different statins on the structure and function of human gut bacterial community – Zhao et al.PLoS ONE

Human vaginal microbiome

* A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women – Stennett et al.PLoS ONE

Animal experiments

Polysaccharide extracted from WuGuChong reduces high-fat diet-induced obesity in mice by regulating the composition of intestinal microbiota – Wang et al.Nutrition & Metabolism

Animal microbiome

Intestinal microbes: an axis of functional diversity among large marine consumers – Scott et al.Proceedings of the Royal Society B

Plant, root, and soil microbiome

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: Accelerated biodegradation or toxicity? – Katsoula et al.FEMS Microbiology Ecology

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species – Yao et al.Applied Soil Ecology

Water and extremophile microbiome

* Preprint: New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal – Coutinho et al.


Ten simple rules for providing effective bioinformatics research support – Kumuthini et al.PLoS Computational Biology

Finally, remember that physical isolation doesn’t have to mean social isolation. Call someone you haven’t talked to in a while, I’m sure they’ll appreciate it! You’re doing great 😀

April 2, 2020

Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

Lung function and microbiota diversity in cystic fibrosis – Cuthbertson et al. – BMC Microbiome

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Yu et al. – PLOS Medicine

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports


Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports

March 27, 2020

We begin with a few updates about the recent research news about COVID 19 and how as a scientist you might be able to help. As a result of the global lock down, many conferences and seminars have moved online. You will find some of the microbiome-related online events in today’s post. Please also have a look at a special issue of the Philosophical Transactions of the Royal Society for conceptual challenges in microbial community ecology.

Coronavirus vaccines: five key questions as trials begin – Nature News

How blood from coronavirus survivors might save lives – Nature News

COVID-19 Pandemic: Scientist volunteer form

An initiative to redirect scientific resources towards the fight against COVID-19

Virtual Events
Virtual Conference: 6th Annual Translational Microbiome Conference

Guts & Bugs: A virtual GI seminar series by Edelblum Lab

Let’s go viral: online microbiology seminars in partnership with International Society of Microbial Ecology
Schedule can be found via Twitter #MicroSeminar @MicroSeminar

General microbiome
SPECIAL ISSUE: Phillosophical Transactions of the Royal Society B : Conceptual challenges in microbial community ecology

Human respiratory microbiome
Review: Respiratory microbiome and epithelial interactions shape immunity in the lungs – Invernizzi et al. – Immunology

Human oral microbiome
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome – Gao et al. – npj Biofilms and Microbiomes

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers – Sato et al. – npj Biofilms and Microbiomes

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile – Chatzigiannidou et al. – npj Biofilms and Microbiomes

Dysbiotic oral microbiota and infected salivary glands in Sjögren’s syndrome – Alam et al. – PLOS ONE

Animal experiments
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth – Consuegra et al. – PLOS Biology

Bacterially produced metabolites protect C. elegans neurons from degeneration – Urrutia et al. – PLOS Biology

Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra – Rathje et al. – PLOS Pathogens

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice – Jangid et al. – PLOS ONE

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production – Osbelt et al. – PLOS Pathogens

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme – Langner et al. – PLOS ONE

Animal microbiome
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity – Edenborough et al. – PLOS ONE

Plant, root, and soil microbiome
Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants – Passera et al. – Science of The Total Environment

Book Chapter: Rhizobacteria Versus Chelating Agents: Tool for Phytoremediation – Kaur et al. – Microbial Technology for Health and Environment

Book Chapter: Applications of Microorganisms in Agriculture – Doley et al. – Microbial Technology for Health and Environment

Plant Invasion Has Limited Impact on Soil Microbial alpha Diversity: A Meta-Analysis – Custer & van Diepen – Diversity

Water microbiome
Carbonate facies‐specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT – Ingalls et al. – Geobiology

The microbiome of modern microbialites in Bacalar Lagoon, Mexico – Yanez-Montalvo et al. – PLOS ONE

Food microbiology
Variations in Fungal Community and Diversity in Doushen With Different Flavors – Luo et at. – Frontiers in Microbiology

MetaBridge: An Integrative Multi‐Omics Tool for Metabolite‐Enzyme Mapping – Blimkie et al. – Current Protocols in Bioinformatics

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA – McClenaghan et al. – PLOS ONE

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph – Gautreau et al. – PLOS Computational Biology

The Community Simulator: A Python package for microbial ecology – Marsland et al. – PLOS ONE

Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilusgroup using multiplex PCR – You & Kim – PLOS ONE

Pathogens and microbiome
Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells – Custodio et al. – PLOS Pathogens

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation – Wiles et al. – PLOS Biology

March 26th, 2020

This is my first post on the site! There weren’t a lot of alerts today, so I dug around for other papers I can find. Today’s digest includes mostly human microbiome research, most notably a study identifying a staph peptide that induces acute exacerbation of pulmonary fibrosis, as well as a very diverse epidemiological study of the impact of diet on the gut microbiome in the United States.

General Human Microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population  – Peters, B.A., Yi, S.S., Beasley, J.M. et al. – ISME

Microbiome in Pregnancy and Birth

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring – Vuillermin, P.J., O’Hely, M., Collier, F. et al. – Nature Communications

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta, O., Ghosh, T.S., Kothidar, A. et al. – Microbial Ecology

Translational human microbiome research

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza, C.N., Kobayashi, T., Yasuma, T. et al. – Nature Communications

Effect of probiotics during vonoprazan‐containing triple therapy on gut microbiota in Helicobacter pylori infection: A randomized controlled trial – Kakiuchi et al. – Helicobacter

Rosuvastatin alters the genetic composition of the human gut microbiome – Kummen, M., Solberg, O.G., Storm-Larsen, C. et al. – Scientific Reports

Microbiome and Cancer

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long, S., Yang, Y., Shen, C. et al. – npj Biofilms and Microbiomes

Plant microbiome

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations – Newberry et al. – Environmental Microbiology

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L) – Alok, D., Annapragada, H., Singh, S. et al. – Scientific Reports

Soil microbiome

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi – Ferreira et al. – Microbial Ecology

Bioinformatics/Sequencing analysis methods

Joining Illumina paired-end reads for classifying phylogenetic marker sequences – Liu et al. – BMC Bioinformatics

M2IA: a Web Server for Microbiome and Metabolome Integrative Analysis – Ni et al. – Bioinformatics


Alcohol pretreatment of stools effect on culturomics – Afouda, P., Hocquart, M., Pham, T. et al. – Scientific Reports

Pre-prints on bioRxiv to look forward to

Infant gut microbiome

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics – West et al. (Side note: The Banfield lab produces a lot of good work!)

Laboratory work on bacterial motility in the gut

Bacterial Swarmers exhibit a Protective Response to Intestinal Stress – Chen et al.

Long-read sequencing of gut mycobiome

Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation – Hanafy et al.


HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data