November 6, 2020

Shalom from Israel!

While the eyes of the world are looking at the US elections results, it’s good to know that the world of microbiome research is stable and produces great scientific discoveries. So stop refreshing the news websites, grab yourself a cup of cofee and enjoy your Saturday.

Today’s digest has some great papers about memory in microboimes, factors that shapes bacterial growth, infant skin microbial communities, degraded soils restoration using self-assembly communities, songbirds microbiome, antiSMASH3 is out (!), useful youtube video for metagenome ML analysis in MATLAB and more. Reminding those of you who are intrested in agriculture-related microbioe studies to stop by and follow my bot agmicroPapers

General microbiology

Memory shapes microbial populations, Chaitanya S Gokhale , bioRxiv

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness, Emily C. Pierce, Nature Microbiology

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth, Esha Atolia , mBio

Human microbiome

Host variables confound gut microbiota studies of human disease, Ivan Vujkovic-Cvijin, Nature

Infant Skin Bacterial Communities Vary by Skin Site and Infant
Age across Populations in Mexico and the United States
, Melissa B. Manus, mSystems

Plant and soil microbiome

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins, Nick C. Snelders, Nature Plants

Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant, Jiayin Feng, Soil Ecology Letters

Restoring degraded microbiome function with self-assembled communities, Carlos Fernando Gutierrez Landazuri , FEMS Micro. Eco.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum, Myrto Tsiknia, FEMS Micro. Eco.

Animal microbiome

Evidence supporting the microbiota–gut–brain axis in a songbird, Morgan C. Slevin, Biology Letters

Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal’s Eyed Turtle (Sacalia bealei) by 16S rRNA Gene Sequencing, Jonathan J. Fong , Front. Micro.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests, Markus Oberpaul , Front. Micro.


EUKulele: Taxonomic annotation of the unsung
eukaryotic microbes
, Arianna I. Krinos, JOSS

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes, Kai Blin, Nucleic Acids Research

**Youtube Video- Microbiome: How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data

**Help questionnaire! Natural Products – Data Repositories Questionnaire

July 16, 2020

Greeting everyone from the boiling hell southern Spain tourns every Summer.

Today we have a lot of soil microbiome in general. Also PARGT, a new software tool for predicting antimicrobial resistance in bacteria. And new insight in the relatioship between blood type and bacteria.

General microbiome

Blood type and the microbiome- untangling a complex relationship with lessons from pathogens – Kathleen L Arnolds et al. – Current Opinion in Microbiology

In vivo synthesis of bacterial amyloid curli contributes to joint inflammation during S. Typhimurium infection – Amanda L. Miller et al. – PLOS PATHOGENS

Human respiratory microbiome

Proteomic advances in salivary diagnostics – Eftychia Pappa et al. – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Human gut microbiome

The Influence of Gut and Tumor Microbiome on Pancreatic Cancer Outcomes – Natalia Khalaf MD et al. – Gastroenterology

Animal microbiome

Inulin alleviates hypersaline-stress induced oxidative stress and dysbiosis of gut microbiota in Nile tilapia (Oreochromis niloticus) – Li Zhou et al. – Aquaculture

Water and extremophile microbiome

Microbial Community Composition and Function in Sediments from the Pearl River Mouth Basin – Ye Chen et al.Journal of Ocean University of China

Protist Interactions and Seasonal Dynamics in the Coast of Yantai, Northern Yellow Sea of China as Revealed by Metabarcoding – Yingjun Fu etl al. – Journal of Ocean University of China volume

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming – Zhen-Zhen Zheng et al. – Nature Communications

Pre-print Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance – Ankita Kothari et al. – bioRxiv

Plant, root, and soil microbiome

Review – Can interaction between silicon and non–rhizobial bacteria benefit in improving nodulation and nitrogen fixation in salinity–stressed legumes? A review – Hassan Etesami – Rhizosphere

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation – Jun Zhao et al. – Applied Microbiology and Biotechnology

Microbial clicks and combobulation: integrating microbes without passports and visas for managing soilborne diseases – Sanogo Soum –
Archives of Phytopathology and Plant Protection

Arbuscular mycorrhizal fungi improve mineral nutrition and tolerance of olive tree to Verticillium wilt – Boutaj Hanane – Archives of Phytopathology and Plant Protection

Responses of microbial communities and metabolic activities in the rhizosphere during phytoremediation of Cd-contaminated soil – Chenjing Liu et al. – Ecotoxicology and Environmental Safety

MnO2/tourmaline composites as efficient cathodic catalysts enhance bioelectroremediation of contaminated river sediment and shape biofilm microbiomes in sediment microbial fuel cells – Wei Li et al. – Applied Catalysis B: Environmental

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation – Jun Zhao et al. Applied Microbiology and Biotechnology

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond – Wen-hua Zhou et al. – Applied Microbiology and Biotechnology

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato et al. – PLOS ONE

Built environment

Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses – Jantharadej, Krittayapong et al. – Journal of Environmental Science and Health

Determination of the inhibitory concentration level of fat, oil, and grease (FOG) towards bacterial and archaeal communities in anaerobic digestion – Muhammad Usman et al. – Renewable and Sustainable Energy Reviews


PARGT: a software tool for predicting antimicrobial resistance in bacteria – Abu Sayed chowdhury et al. – Scientific Reports

Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing – Phillip R. Myer et al. – PLOS ONE

June 28, 2020

Greetings from Wiltshire, England!

Today’s digest brings a little bit of everything. We’ve been cataloguing the latest COVID-19 publications during this pandemic, and today I’m please to bring you a paper combining both COVID-19 and microbiome research!

Elsewhere, there are plenty of environmental microbiome publications, including a great paper on the challenges of studying microbiology in space, an analysis of how aerosols spread COVID-19 and other infectious agents in dental practices, and plenty of articles on various aspects of soil microbiomes.

I hope everyone’s coping well during these times. On a personal level, I’m delighted to be returning to the lab this week to resume my PhD research into gut microbiomes and cancer. I’m glad to be back, but worried about how my pipetting skills have suffered during my time off!

Stay safe, and happy reading!


Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – He et al.Frontiers in Microbiology

Preprint: Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry – Ozono et al.

Human vaginal microbiome

Novel Potential Probiotic Lactobacilli for Prevention and Treatment of Vulvovaginal Infections – Kumherová et al. – Probiotics and Antimicrobial Proteins

Preprint: The structure and diversity of strain level variation in vaginal bacteria –Tortelli et al.

Human gut microbiome

Early exposure to food contaminants reshapes maturation of the human brain-gut-microbiota axis – Sarron et al.World Journal of Gastroenterology

Luminal microbiota related to Crohn’s disease recurrence after surgery – Hamilton et al.Gut Microbes

Animal experiments

Preprint: The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet – Mims et al.

Animal microbiome

Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice – Kiouptsi et al.Gut Microbes

The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea – Xavier et al.Marine Biology

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus – Ying et al.Current Microbiology

Plant, root, and soil microbiome

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. – Delamuta et al.International Journal of Systematic and Evolutionary Microbiology

Efects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Salam et al.Bioresources and Bioprocessing

Differences in soil microbial communities and enzyme activity due to the application of bioslurry under cultivation – Mofokeng et al.South African Journal of Plant and Soil

Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions – Jacobs et al.Diversity

Water and extremophile microbiome

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location – Schulhof et al.Molecular Ecology

Preprint: Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific – Rojas-Jimenez et al

Built environment

Preprint: Evaluating aerosol and splatter following dental procedures – Allison et al.

Microbes in space

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology – Chen et al.BioMed Research International

Food microbiology

Swine Methicillin-resistant Staphylococcus aureus carrying toxic-shock syndrome toxin gene in Hong Kong, China – Sapugahawatte et al. – Emerging Microbes and Infections

Probiotics / prebiotics

Moving from probiotics to precision probiotics – Veiga, et al. – Nature Microbiology

Phages and viruses

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia – Gaccioli et al. – Nature Microbiology


Developing standards for the microbiome field – Amos et al.Microbiome

Microbes in the news

Team Examines Microbiome of Marine Invertebrate That Produces Anticancer CompoundTechnology Networks

Bacteria live on our eyeballs — and understanding their role could help treat common eye diseasesYahoo! News

May 13, 2020

Happy Wednesday, y’all! Before we get to today’s papers, I wanted to let everyone know about a webinar happening on June 3rd at 12:00 PM E.T. called “Unraveling the link between the gut microbiome, human health, and disease.” Tomoya Yamashita, M.D., Ph.D. from Kobe University Graduate School of Medicine and Meredith Hullar, Ph.D. from the Fred Hutchinson Cancer Research Center will both be speaking. If you’re interested you can register here.

Now onto the highlights! We have some super interesting research to share with you today including an examination of the efficacy of transplanting the human gut microbiota into mice and its impact on studying immunological responses; evidence that early-life intestinal colonizers may influence brain development; and a new tool, pepFUNK, which uses a peptide-centric approach to identify KEGG pathways in metaproteomic datasets. Enjoy!

General microbiome
Human Microbiota-Transplanted C57BL/6 Mice and Offspring Display Reduced Establishment of Key Bacteria and Reduced Immune Stimulation Compared to Mouse Microbiota-Transplantation. Lundberg, R. et al. Scientific Reports.

Review: The role of the microbiome in the neurobiology of social behaviour. Sarkar, A. et al. Biological Reviews.

Pregnancy and early life
Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Brink, L.R. et al. The American Journal of Clinical Nutrition.

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers. Lugli, A.G. et al. FEMS Microbiology Ecology.

Human respiratory microbiome
Bioorthogonal Non-Canonical Amino Acid Tagging Reveals Translationally Active Subpopulations of the Cystic Fibrosis Lung Microbiota. Valentini, T.D. et al. Nature Communications.

Human gut microbiome
Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Zhou, X. et al. Diabetes.

Berberine and Its Structural Analogs Have Differing Effects on Functional Profiles of Individual Gut Microbiomes. Li, L. et al. Gut Microbes.

Animal experiments
Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Swann, J.R. et al. Metabolites.

Bifidobacteria Shape Host Neural Circuits During Postnatal Development by Promoting Synapse Formation and Microglial Function. Luck, B. et al. Scientific Reports.

Glycerol Monolaurate, an Analogue to a Factor Secreted by Lactobacillus, Is Virucidal Against Enveloped Viruses, Including HIV-1. Welch, J.L. et al. mBio.

Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. Burgess, S.L. et al. The Journal of Clinical Investigation.

The Protective Effects of 2′-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion. Wang Y. et al. Nutrients.

Capsaicin Improves Glucose Homeostasis by Enhancing Glucagon-Like peptide-1 Secretion Through the Regulation of Bile Acid Metabolism via the Remodeling of the Gut Microbiota in Male Mice. Hui, S. et al. FASEB Journal.

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells. Schaupp L. et al. Cell.

Intratumoral Accumulation of Gut Microbiota Facilitates CD47-based Immunotherapy via STING Signaling. Shi, Y. et al. Journal of Experimental Medicine.

Animal microbiome
Housefly (Musca domestica L.) associated microbiota across different life stages. de Jonge, N. et al. Scientific Reports.

Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Deboutte, W. et al. PNAS.

Bayesian Modeling Reveals Host Genetics Associated With Rumen Microbiota Jointly Influence Methane Emission in Dairy Cows. Zhang, Q. et al. ISME Journal.

Review: The role of the gut microbiome in sustainable teleost aquaculture. Perry, W.B. et al. Proceedings of the Royal Society B.

Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Wikberg E.C. Animal Behaviour.

Plant, root, and soil microbiome
Global Warming Shifts the Composition of the Abundant Bacterial Phyllosphere Microbiota as Indicated by a Cultivation Dependent and Independent Study of the Grassland Phyllosphere of a Long-Term Warming Field-Experiment. Aydogan, E.L. et al. FEMS Microbiology Ecology.

Probiotics / prebiotics
A Human-Origin Probiotic Cocktail Ameliorates Aging-Related Leaky Gut and Inflammation via Modulating the Microbiota/Taurine/Tight Junction Axis. Ahmadi, S. et al. JCI Insight.

SHOGUN: A Modular, Accurate, and Scalable Framework for Microbiome Quantification. Hillmann, B. et al. Bioinformatics.

pepFunk: A Tool for Peptide-Centric Functional Analysis of Metaproteomic Human Gut Microbiome Studies. Simopoulos, C.M.A. et al. Bioinformatics.

Microbes in the news
Mapping the Microbiome in Saliva of COVID-19 Patients.

Inside the Belly of the Horse – Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health.

April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!


Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale –