July 17, 2020

Human microbiome

Covid-19: disinfectants and sanitisers are changing microbiomes. Ajit Singh.
BMJ.

Probiotics and COVID-19: one size does not fit all. Joyce WY Mak. The Lancet Gastroenterology & Hepatology.

Probiotics and COVID-19. Eric Giannoni. The Lancet Gastroenterology & Hepatology.

Animal microbiome
The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis. Emma S. Winkler.Cell

Built-in environment
Bed bugs shape the indoor microbial community composition of infested homes. Madhavi L.Kakumanua. Science of the Total Environment.

Pre-print
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. Laura Glendinning. bioRxiv.

Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria. Sean Michael Kearney. bioRxiv

Microbes in the news
The human microbiome: Everything you need to know about the 39 trillion microbes that call our bodies home. Mun-Keat Looi. ScienceFocus

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

Bioinformatics

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

July 15, 2020

There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

Perspective: Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology & Hepatology

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine

July 11, 2020

Good morning everyone. Today’s digest includes various interesting articles such as: 1) mNGS-based approach for broad-range detection of pathogens associated with CNS infections, 2) dynamics of diarrheal pathogenesis and antimicrobial resistance transmission using gut microbiome and resistome profiling, 3) comparison urinary and bladder mucosa-associated microbiome composition in bladder cancer patients, 4) regulation of vaginal microbiome composition and stability by ovarian hormones, diet and exercise, 5) Chokeberry polyphenols can reduce the body weight of HFD-fed rats by accelerating energy homeostasis and thermogenesis in interscapular brown adipose tissue, 6) Comparison of taxonomic composition and diversity of bacterial and fungal communities in synanthropic and non-synanthropic mound-building mouse, and 7) an information retrieval system for large metagenomic datasets to recover missing content from genome bins. Enjoy reading. Happy weekend.

General microbiome

Commentary: mSphere of Influence: Translating Gut Microbiome Studies To Benefit Human Health – Anna M. Seekatz – mSphere

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting – Mohammad Rubayet Hasan – Scientific Reports

Human microbiome

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter – Rituparna De – Gut Pathogens

Bladder cancer-related microbiota: examining differences in urine and tissue samples– Bassel Mansour – Scientific Reports

Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise – Stephanie D. Song – mSphere

Dynamics of the lung microbiome in intensive care patients with chronic obstructive pulmonary disease and community-acquired pneumonia – Wei-Chang Huang – Scientific Reports

Animal microbiome / Animal experiments

The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats – Yue Zhu – Nutrition and Metabolism

Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers – Shengru Wu – Journal of Animal Science and Biotechnology

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginicaAdrian Britt – Scientific Reports

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies – Barbora Bendová – BMC Microbiology

Fruit and vegetable microbiome

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis – Antonio Benítez-Cabello – Scientific Reports

Plant, root and soil microbiome

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules – Dan Naylor – mBio

Water microbiome

Metagenomic water quality monitoring with a portable laboratory – Kishor Acharya – Water Research

Methods

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity – C. Titus Brown – Genome Biology

July 9, 2020

Good morning! Today there are not many papers, but there are two interesting highlights. The first being a COVID paper analysing the immunological profiles of patients, suggesting an immune-based therapeutic intervention may be the way to go. The second paper analysing the oral microbiome in oral cancer patients, showing significant alterations in diversity and specific genuses in these patients.

Enjoy!

COVID-19

Immunological and inflammatory profiles in mild and severe cases of COVID-19. Song et al. Nature Communications.

Human microbiome

Oral microbial dysbiosis and its performance in predicting oral cancer. Su et al. Carcinogenesis.

Animal microbiome

Potential of indigenous Bacillus spp. as probiotic feed supplements in an extruded low‐fish‐meal diet for juvenile olive flounder, Paralichthys olivaceus. Niu et al. Journal of the World Aquaculture Society.

Animal experiments

Glyphosate-based herbicides influence antioxidants, reproductive hormones and gut microbiome but not reproduction: A long-term experiment in an avian model. Ruuskanen et al. Environmental pollution.

Evidence of Microbiome-Drug Interactions Between the Antimalarial Lumefantrine and Gut Microbiota in Mice. Ippolito et al. The American Journal of Tropical Medicine and Hygiene.

Plant, root and soil microbiome

The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants. Xu et al. Society for Applied Microbiology.

Water and extremophile microbiome

Host and environmental determinants of microbial community structure in the marine phyllosphere. Vogel et al. PLOS ONE.

July 6, 2020

God morgon!

Good morning from Sweden. Another new week and another new digest! Today’s digest is very light with only a few articles. There is an interesting preprint which reports that the SARS-CoV-2 spike protein variant D614G leads to increased infectivity and the virus might have acquired this mutation during human-to-human transmission as this mutation is not seen in the original virus that infects the non-human hosts. This might be the reason why about 97% of the nCoV19 isolates have this mutation. However, the good news is that the neutralizing antibodies against the wildtype virus still retain the ability to target this mutant virus. Another interesting commentary published in Microbiome journal revisits important concepts in microbiome biology and is a must-read for all the microbiome enthusiasts. Elsewhere in the digest is a study on microbial succession in deep-sea hydrothermal vents, microbial communities of small brown planthopper (Laodelphax striatellus) and Shrimp (Litopenaeus vannamei), and thermophilic digestion of biowaste.

Happy reading and have a great week!

COVID 19

Preprint: SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain – Leonid Yurkovetskiy, et al.

General Microbiome

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle – Yanting Wang, et al. – Microbiome

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste – Stefan Dyksma, et al. – Microbiome

Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations – Xing-Zhi Duan, et al. – Microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg, et al. – Microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Jialin Hou, et al. – Microbiome

 

July 5, 2020

Pregnancy and early life
Natural environments in the urban context and gut microbiota in infants – Neilsen et al. – Environment International

Human nearly-sterile sites
Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression – Parhi et al. – Nature Communications

Enrichment of the airway microbiome in people living with HIV with potential pathogenic bacteria despite antiretroviral therapy – Rofael et al. – EClinicalMedicine

Human microbiome in vitro and ex vivo experiments
Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro – Mahalak et al. – PLOS One

Animal experiments
Alterations of gut microbiota and serum bile acids are associated with parenteral nutrition-associated liver disease – Wang et al. – Journal of Pediatric Surgery

Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs – Vigors et al. – Animal

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses – Wan et al. – BMC Veterinary Research

Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms – Li et al. – Nature Communications

Animal microbiome
Review: The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease – Wernimont et al. – Frontiers in Microbiology

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota – Sugden et al. – Microbial Ecology

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia – Segura et al. – PLOS One

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China – Ajene et al. – PLOS One

Plant, root, and soil microbiome
Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices – Zambounis et al. – Archives of Microbiology

Water and extremophile microbiome
The Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA – Lusty and Gobler – Toxins

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network – Luo et al. – FEMS Microbiology Ecology

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD) – Adyasari et al. – PLOS One

The contribution of microbial communities in polymetallic nodulesto the diversity of the deep-sea microbiome of the Peru Basin(4130–4198 m depth) – Molari et al. – Biogeosciences

Probiotics / prebiotics
Review: Toward a systematic design of smart probiotics – Choudhary and Mahadevan – Current Opinion in Biotechnology

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated In Vitro Approach – Van den Abbeele et al. – Nutrients

Bioinformatics
Review: What Is Metagenomics Teaching Us, and What Is Missed? – New and Brito – Annual Review of Microbiology

July 1, 2020

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


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

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

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

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

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

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

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


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

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


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

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


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

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

June 29, 2020

Human microbiome

Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study. – Pan et al. – Psychiatry Research

A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents. – Holferson et al. – Scientific Reports

Gut microbiome

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

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. – Hughes et al. – Nature Microbiology

Cancer and the microbiome. – Ashray Gunjur. The Lancet

Food microbiology

Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread – Reese et al. – mSphere

Plant, root and soil microbiome

Effects of zinc pollution and compost amendment on the root microbiome of a metal tolerant poplar clone. – Guarino et al. – Frontier in Microbioloy

New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. – Tang et al. – The ISME Journal

Language of plant-microbe-microbe interactions in rhizospheric ecosystems. – Khare et al. – Molecular Aspects of Plant Benefitial Microbes in Agriculture

Environmental microbiology

Editorial: Microbial Ecology in Reservoirs and Lakes. Zhang et al. – Frontier in Microbiology

Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. – Rodriguez and Duran – Frontiers in Bioengineering and Biotechnology.

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!

COVID-19

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

Techniques

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