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 12, 2020

Buenos dias!! Greetings from Spain.

Today we can highlight a very interesting article of gut–brain modulation of a monkey model of human depression, MELODY a new trial to improve the future microbiome of the offspring of mothers with Crohn’s disease, or how It’s the fertilization the main agent in rhizosphere composition.

I hope you enjoy reading this as much as I did making it!
Stay safe, Jose


Pre-print: Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals – Manas Ranjan Praharaj et al. – bioRxiv

Pre-print: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity – Niko Kohmer et al. – bioRxiv

Pre-print: The role of high cholesterol in age related COVID19 lethality. – Hao Wang et al. – bioRxiv

Human vaginal microbiome

Effect of commercial vaginal products on the growth of uropathogenic and commensal vaginal bacteria – Kristin J. Hung et al. – Scientific Reports

Human respiratory microbiome

Differences in airway microbiome and metabolome of single lung transplant recipients – Nirmal S. Sharma et al. – Respiratory Research

Pre-print: Assessing the variation within the oral microbiome of healthy adults – Jacob T. Nearing et al. – bioRxiv

Microbiome profile associated with malignant pleural effusion – Samira Shojaee et al. – PLOS ONE

Composition and function of oral microbiota between gingival squamous cell carcinoma and periodontitis – Yuchao Li et al. – Oral Oncology

Esophageal microbiome signature in patients with Barrett’s esophagus and esophageal adenocarcinoma – Loris Riccardo Lopetuso et al. – PLOS ONE

Human gut microbiome

Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of GutMicrobiota – Tuncil, Y. E et al. – mSphere

Intestinal parasites in rural communities in Nan Province, Thailand: Changes in bacterial gut microbiota associated with minute intestinal fluke infection – Ajala Prommi et al. – Cambridge University Press

Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease – Michelle R et al. – Journal of the American Society of Nephrology

The gut microbiome modulates gut–brain axis glycerophospholipid metabolism in a region-specific manner in a non-human primate model of depression – Peng Zheng et al. – Molecular Psychiatry

A dietary intervention to improve the microbiome composition of pregnant women with Crohn’s disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design – Peter Inga et al. – Contemporary Clinical Trials Communications

Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease – Meng Li et al. – Scientific Reports

Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males – Gerben D. A. Hermes et al. – Scientific Reports

Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn’s disease – Anna Strömbeck et al. – BMC Gastroenterology

Human skin microbiome

Diversity of navel microbiome in young adults Free – Shreya Shah et al. – Journal of Medical Microbiology

Animal experiments

Wild primate microbiomes prevent weight gain in germ-free mice – Dimitrios N. Sidiropoulos et al. – Animal Microbiome

Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens – Karen K. Dittmann et al. – Applied and Environmental Microbiology

Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus – B N Smith et al. – Journal of Animal Science

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection – Qiang Zhang et al. – Genome Biology

Pre-print: Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – Aaron McKenna et al. – bioRxiv

Administration of Bifidobacterium bifidum CGMCC 15068 modulates gut microbiota and metabolome in azoxymethane (AOM)/dextran sulphate sodium (DSS)-induced colitis-associated colon cancer (CAC) in mice – Qing Wang et al. – Applied Microbiology and Biotechnology

Animal microbiome

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects – My Hanh Le et al. – Scientific Reports

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus) – Geraint Element et al. – Envariomental microbiology

Honeybee microbiome is stabilized in the presence of propolisPerot Saelao et al. – Biology letters

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels – Po-Yu Liu et al. – Scientific Reports

Preprint: Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar) – Yanxian Li et al. – bioRxiv

Plant, root, and soil microbiome

Liming reduces N2O emissions from Mediterranean soil after-rewetting and affects the size, structure and transcription of microbial communities – Eduardo Vázquez et al – Soil Biology and Biochemistry

Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management – Vivian A. Rincon-Florez – Pedobiologia

Seasonal variations in soil microbial communities under different land restoration types in a subtropical mountains region, Southwest China – Denggao Fu et al. – Applied Soil Ecology

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities – Rubab Sarfraz et al. – Chemosphere

Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil – George Mangse et al.– Environmental Pollution

Plant litter amendments in restored wetland soils altered microbial communities more than clay additions – Christine E. Maietta et al. – Soil Biology and Biochemistry

Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems – Mikhail V. Semenov et al. – Applied Soil Ecology

Effect of compost amendment and bioaugmentation on PAH degradation and microbial community shifting in petroleum-contaminated soil – Manli Wu et al. – Chemosphere

Review: The use of -omics tools for assessing biodeterioration of cultural heritage: A review – GutarowskaBeata – Journal of Cultural Heritage

Water and extremophile

Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells – Sara Gallego et al – Science of The Total Environment

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea – Qing-Lei Sun et al. – Microorganisms

Glacial microbiota are hydrologically connected and temporally variable – Karen A Cameron et al. – Enviromental microbiology

Built environment

The microbiome driving anaerobic digestion and microbial analysis – Jun Wei Lim et al. – Advances in Bioenergy


MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data – Nathanael J. Bangayan et al. – Microorganisms

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia – Matthew G Jones et al. – Genome Biology

TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples – Mathias Kuhring et al. Journal of Proteome Research

Review: The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health – Ameen Eetemadi et al. – Frontiers in Microbiology

General microbiology

Review: Diversity, ecology and evolution of Archaea – Brett J. Baker et al – Nature Microbiology

Microbes on the market

Microbiome Sequencing Services Market 2020-2024 – husain – NJ MMA News

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 – FierceBiotech.com