Good morning everyone! In today’s microbiome digest we have several reviews and research articles focused on the human microbiome, some animal studies, few interesting methods such as Kraken2 for 16S rRNA analysis, and Convolutional Neural Network for prediction of host phenotypes from microbial samples. Enjoy reading!!

General microbiome

Review: CRISPR screens in the era of microbiomes – François Rousset – Current Opinion in Microbiology

Chapter: Genetic Transformation of Fusobacterium nucleatum – Akihiro Yoshida – Methods in Molecular Biology

Perspective: Gut microbiota: a potential therapeutic target for Parkinson’s disease – José Fidel Baizabal-Carvallo – Neural Regeneration Research

Processing has differential effects on microbiota accessible carbohydrates in whole grains during in vitro fermentation – Caroline Smith – Applied Environmental Microbiology

Human gut microbiome

Gut microbiota and oral contraceptive use in overweight and obese patients with polycystic ovary syndrome – Nesrin Damla Eyupoglu – The Journal of Clinical Endocrinology and Metabolism

Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population – Siqi Ye – The Journal of Dermatology

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma – Gianluca Ianiro – Nature Communications

Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism – Amira Metwaly – Nature Communications

Review: The potential role of the gut microbiota in shaping host energetics and metabolic rate – Elle C Lindsay – Journal of Animal Ecology

Oral and respiratory microbiome

Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment– Marlos Barbosa-Ribeiro – Clinical Oral Investigation

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals – Judith Neukamm – BMC Biology

Comparing the nasal bacterial microbiome diversity of allergic rhinitis, chronic rhinosinusitis and control subjects – Weigang Gan – European Archives of Oto-Rhino-Laryngology

Maternal Oral Health Influences Infant Salivary Microbiome – K. Ramadugu – Journal of Dental Research

Animal microbiome / Animal experiments

Dietary supplementation of sodium sulfate improves rumen fermentation, fiber digestibility and plasma metabolome through modulating rumen bacterial communities in steers – Yuchao Zhao – Applied Environmental Microbiology

Salmonella enterica serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine – Danisa M Bescucci – Applied Environmental Microbiology

Germ-Free Conditions Modulate Host Purine Metabolism, Exacerbating Adenine-Induced Kidney Damage – Eikan Mishima – Toxins

Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression – Jichun Chen – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied Environmental Microbiology

Water and extremophile microbiome

Dissolved microcystin release coincident with lysis of a Microcystis-dominated bloom in western Lake Erie attributed to a novel cyanophage – McKindles et al – Applied Environmental Microbiology

Methods

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Chapter: Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Derek Reiman – Artificial Neural Networks

Techniques

Review: Application of Next Generation Sequencing in Laboratory Medicine – Yiming Zhong – Annals of laboratory medicine

Good morning! Today’s post features a wide variety of interesting topics ranging from the role of the microbiome in attacking cancerous tumors, the potential use of extremophiles in Mars’ habitability and the association of worsening of NAFLD with cardiometabolic function. There is also a nice symposium report on the role of probiotics to a healthy microbiota and a fascinating look into the bacterial nano-universe using Cryo-ET.

Enjoy!!

COVID-19

An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques OPEN. Liqiang Feng, et al. Nature

HUMAN GUT MICROBIOME

Association of worsening of nonalcoholic fatty liver disease with cardiometabolic function and intestinal bacterial overgrowth: A cross-sectional study. Marília Marques Pereira Lira, et al. PLOS ONE

[HTML] Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. S Duranti, et al. – Scientific Reports

[PDF] The role of probiotics on the roadmap to a healthy microbiota: a symposium report. S Lockyer, et al. – Gut Microbiome

PLANT, ROOT AND SOIL MICROBIOME

Preprint: [PDF] Geological Characteristics of Close Geographical Related Vineyards Influence Microbiomes of Two Soil Depth Profiles With Potential Impacts on Wine Quality. L Nerva, et al. Research Square

ANIMAL EXPERIMENTS

How the environment and the microbiome jointly shape the body. Phys.Org

ANIMAL EXPERIMENTS

News article: New insight into microbiome’s role in attacking cancerous tumours. THE WEEK

PHAGES AND VIRUSES

News article: HIV enters deep sleep in people who naturally control the virus. Nature

Preprint: Induction of selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir. Shringar Rao, et al. bioRxiv

WATER AND EXTREMOPHILE MICROBIOME

[PDF] Can Halophilic and Psychrophilic Microorganisms Modify the Freezing/Melting Curve of Cold Salty Solutions? Implications for Mars Habitability. L Garcia-Descalzo, et al.- Astrobiology

BUILT ENVIRONMENT

Metagenomic characterization of microbial communities on plasticized fabric materials exposed to harsh tropical environments. O Radwan, et al. – International Biodeterioration & Biodegradation

BIOINFORMATICS

Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease. Y Qian, et al. – Brain

[HTML] CRISPR screens in the era of microbiomes. F Rousset, et al. – Current Opinion in Microbiology

[HTML] Microbial single-cell omics: the crux of the matter. AK Kaster, et al. – Applied Microbiology and Biotechnology

[HTML] Bionetworks, system biology, and superorganisms. M Nicoletti – Insect-Borne Diseases in the 21st Century

TECHNIQUES

[HTML] Exploring the bacterial nano-universe. N Söderholm, et al. – Current Opinion in Structural Biology

Good morning! Today has a great nature paper on bacterial metabolic crossfeeding that can result in altered egg laying and reproducing behaviour, and additionally a paper showing how bacterial probiotics induce anergy in mice with Cow’s Milk allergy.

General microbiome

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour, Henriques et al, Nature.

The Impact of the Postpartum “Doing-the-Month” Practice on Human Milk Microbiota: A Pilot Study in Taiwan, Chen et al. Microorganisms.

Vaginal microbiota

Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota, Agarwal et al, PLOS biology.

Human gut microbiome

How Serotonin Level Fluctuation Affects the Effectiveness of Treatment in Irritable Bowel Syndrome, Vahora et al. Cureus.

Animal experiments

Three Candidate Probiotic Strains Impact Gut Microbiota and Induce Anergy in Mice with Cow’s Milk Allergy. Esber et al. Public and environmental Health Microbiology.

Plant, root and soil microbiome

Role of environmental factors in shaping the soil microbiome, Islam et al. Environmental Science and Pollution research.

Bioinformatics

Predictive analysis methods for human microbiome data with application to Parkinson’s disease, Dong et al, PLOS One.

God morgon!

Good morning from Sweden.

I am sure there are a lot of labs and scientists with interesting therapeutic options against COVID19, but unable to do so due to lack of BSL-3 facilities. Good news for them as today’s digest carries a preprint where some researchers show that a recombinant vesicular stomatitis virus expressing nCoV spike protein can be used to evaluate the potential of anti-spike antibodies. They designed a specific assay which could be modified to work out for evaluation of other therapeutics. Continuing with viruses, there is another preprint that delineates a new strategy to design effective vaccines against Ebola virus.

New research published in Microbiome journal describes the effect of antimicrobials on salivary microbiota and how gut microbiota may be implicated in regulating autism-like behaviour through vitamin B6 homoeostasis.

Elsewhere in the digest is new research featuring a new technique ‘Protoblock’ for increasing reproducibility in pathology samples, biocontrol of plant disease using bacteria, on-site detection of Genus Clavibacter, and the basis of cell polarity in bacteria.

Happy reading and have a great week!

Preprint: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein – Hideki Tani, et al.

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition – Sajan C. Raju, et al, Microbiome

The gut microbiota regulates autism-like behavior by mediating vitamin B₆ homeostasis in EphB6-deficient mice – Ying Li, et al, Microbiome

Preprint: Scaffold-scaffold interactions regulate cell polarity in a bacterium – Wei Zhao, et al.

Preprint: Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines – Linling He, et al.

Preprint: Multiplex recombinase polymerase amplification (RPA) assay developed using unique genomic regions and coupled with a lateral flow device for rapid on-site detection of genus Clavibacter and C. nebraskensis – Adriana Larrea-Sarmiento, et al.

Preprint: Evaluation of the efficacy of some PGPR bacteria in controlling Fusarium wilt disease Fusarium oxysporum f.sp. lycopersici on the tomato plant – Halima Z Hussein and Shaker I Al-Dulaimi.

Preprint: Mutually Beneficial Symbiosis Between Human and Gut-Dominant Bacteroides Species Through Bacterial Assimilation of Host Mucosubstances – Masahiro Sato

Protoblock – A biological standard for formalin fixed samples – Yensi Flores Bueso, et al, Microbiome

Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate – Nguyen K. Nguyen, et al, Microbiome

COVID-19

Human organ chip-enabled pipeline to rapidly repurpose therapeutics during viral pandemics – Si et al. – bioRxiv

FDA approved calcium channel blockers inhibit SARS-CoV-2 infectivity in epithelial lung cells – Straus et al. – bioRxiv

Human oral microbiome

Removal of Dental Plaque by Ultrasonic Toothbrushes – Siddharth et al. – Journal of Critical Reviews

Cigarette smoking and opium use in relation to the oral microbiome in Iran – Zenei Wu et al. – Cancer Research

Animal experiments

Gut microbiome alterations induced by TBT exposure are associated with increased body weight, impaired glucose and insulin homeostasis and endocrine disruption in mice – Zhan et al. – Environmental Pollution

Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation – Haberecht et al. – AMB Express

Animal microbiome

Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows – Berlow et al. – Microbial Ecology

Plant, root and soil microbiome

Plant–microbiome interactions: from community assembly to plant health – Trivedi et al. – Nature Reviews Microbiology *

Healthy soils for healthy plants for healthy humans: How beneficial microbes in the soil, food and gut are interconnected and how agriculture can contribute to human health – Heribert Hirt – EMBO reports

Chemical Ecology of Multitrophic Microbial Interactions: Plants, Insects, Microbes and the Metabolites that Connect Them – Ali et al. – Journal of Chemical Ecology

The role of land management and elevation in shaping soil microbial communities: Insights from the Central European Alps – Praeg et al. – Soil Biology and Biochemestry

Environmental microbiology

Ozone affects plant, insect, and soil microbial communities: A threat to terrestrial ecosystems and biodiversity – Agathokleous et al. – Science Advances *

Microplastics in a dam lake in Turkey: type, mesh size effect, and bacterial biofilm communities – Nihan Tavşanoğlu et al. – Environmental Science and Pollution Research

Bioinformatics

Assembly methods for nanopore‑based metagenomic sequencing: a comparative study – Latorre-Perez et al. – Scientific Reports