October 20,2020

Good morning! Today’s post features several articles relating to the development of the gut microbiome as it pertains to c-section and immune development as well as how dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications. There is also an in-depth article on the impact of microbiota in evolving herd immunity against viral diseases which is especially relevant in the covid-19 pandemic. Enjoy reading and have a great day!

COVID-19

Preprint: The effect of temperature and humidity on the stability of SARS-CoV-2 and other enveloped viruses – Dylan H. Morris, et al. bioRxiv

[PDF] Impact of Microbiota: A Paradigm for Evolving Herd Immunity against Viral Diseases – A Shelly, et al. – Viruses

ORAL MICROBIOME

Preprint: Impact of Commiphora myrrha on bacteria (Streptococcus mutans and Lactobacillus species) related to dental caries – REEM IZZELDIEN, et al. – bioRxiv

[HTML] Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer – S Zhang, et al. – Theranostics

GENERAL MICROBIOME

Microbiota Effects on Carcinogenesis: Initiation, Promotion and Progression -LR Lopez, et al. – Annual Review of Medicine

[HTML] Emerging role of bacterial extracellular vesicles in cancer – A Chronopoulos, R Kalluri – Oncogene

HUMAN GUT MICROBIOME

News Article: Microbiome drug reduces recurrent CDI – Healio

[PDF] Immune development of children born from Caesarean section – Z Munasir, LC Khoe – World Nutrition Journal

[PDF] Caesarean section and gut microbiota in children – AD Widodo, M Juffrie – World Nutrition Journal

Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health -M Fassarella, et al. – Gut

Dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications – J Wu, et al. – Critical Reviews in Food

HUMAN RESPIRATORY MICROBIOME

Preprint: Cystic Fibrosis Acidic Microenvironment Determines Antibiotic Susceptibility and Biofilm Formation of Pseudomonas aeruginosa – Qiao Lin, et al. – bioRxiv

ANIMAL EXPERIMENTS

Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice – H Wang, et al.- Translational Psychiatry

ANIMAL MICROBIOME

[HTML] Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis -N Perveen, et al. – Scientific Reports

PLANT, ROOT AND SOIL MICROBIOME

Preprint: Soil disturbance affects plant growth via soil microbial community shifts – Taylor J Seitz, et al. – bioRxiv

Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana – W Zhang, et al. – Microbial Ecology

WATER AND EXTREMOPHILE MICROBIOME

Role of Extremophiles and Extremophilic Proteins in Industrial Waste Treatment – S Tapadar, et al. – Removal of Emerging …

PHAGES AND VIRUSES

Preprint: The structure of enteric human adenovirus 41 – a leading cause of diarrhoea in children – Karim Rafie, et al. -bioRxiv

Preprint: Clustered Rapid Induction of Apoptosis Limits ZIKV and DENV-2 Proliferation in the Midguts of Aedes aegypti -Jasmine B Ayers, et al. -bioRxiv

BIOINFORMATICS

[PDF] Multi-omics for Biomedical Applications – MS Khan, et al – J Appl Bioanal

September 30, 2020

Hello again everyone! Another change of seasons is upon us and I hope you all remain safe with the upcoming flu season as well as with the continuing covid-19 pandemic. Remember to continue hand washing, social distancing and masking to protect those most vulnerable. Todays post includes more interesting work relating to the gut microbiome with respect to obesity and also as a marker for the disease activity and therapeutic outcome in Inflammatory Bowel Disease. Enjoy!

ORAL MICROBIOME

Preprint: Longitudinal multi-omics along gingivitis development reveal a suboptimal-health gum state with periodontitis-like microbiome – Shi Huang, et al – bioRxiv

PREGNANCY AND EARLY LIFE

News Article: Maternal Microbes Support Fetal Brain Wiring – Nature

HUMAN GUT MICROBIOME

[HTML] Both Gut Microbiota and Differentially Expressed Proteins Are Relevant to the Development of Obesity – Y Li, et al – BioMed Research International

[PDF] How the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease – C Caenepeel, et al – Alimentary Pharmacology & …

ANIMAL MICROBIOME

News Article: Climate warming is altering animals’ gut microbes, which are critical to their health and survival – Fairfield Citizen

PLANT, ROOT AND SOIL MICROBIOME

Soil origin and plant genotype structure distinct microbiome compartments in the model legume …Microbiome – BioMed Central

WATER AND EXTREMOPHILE MICROBIOME

Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina – LM Francisco, E Donati – Environmental Pollution

Fungi and viruses as important players in microbial mats – C Carreira, et al – FEMS Microbiology Ecology

FOOD MICROBIOLOGY

News Article: [PDF] Addition of Coriander during Fermentation of Korean Soy Sauce (Gangjang) Causes Significant Shift in Microbial Composition and Reduction in Biogenic Amine …M Mannaa, et al – Foods

SCIENCE, PUBLISHING AND CAREER

Post-doc in gut microbiome-behaviour research (0.8/1.0 fte) — AcademicTransfer

Space Exploration Plant and Microbiome Learning Sessions start this week – Space Ref

August 29, 2020

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

July 21, 2020

Hello! We are in the midst of an unprecedented heat wave here in Western New York and I hope everyone is enjoying summer in the northern hemisphere. In todays post there is an interesting article by Kyung-Eon Lee, et al on the extracellular vesicle of a gut microbe Paenalcaligenes hominis as a risk factor for vagus nerve-mediated cognitive impairment. There also is a preprint on parthenogenesis in weevils as a possible Wolbachia-density dependent trait to ponder as well as a look at the experimental approaches to investigating the vaginal biofilm microbiome. Enjoy!

COVID-19

Preprint: ACE2-independent interaction of SARS-CoV-2 spike protein to human epithelial cells can be inhibited by unfractionated heparin. Lynda J Partridge, et al. bioRxiv

SARS-CoV-2 is not present in the vaginal fluid of pregnant women with COVID-19. MM Aslan, et al. – The Journal of Maternal…

GENERAL MICROBIOME

Preprint: Targeting methionine synthase in a fungal pathogen causes a metabolic imbalance that impacts cell energetics, growth and virulence. Jennifer Scott, et al. bioRxiv

HUMAN SKIN MICROBIOME

News Article: All-Natural Soap For Nourished And Balanced Microbiome Product Launched

HUMAN VAGINAL MICROBIOME

Experimental approaches to investigating the vaginal biofilm microbiome. PubMed – NIH

HUMAN GUT MICROBIOME

The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment. Kyung-Eon Lee, et al. Microbiome

Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis. MDPI

[PDF] Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study. T Sainz,et al. – Nutrients

ANIMAL MICROBIOME

Preprint: Parthenogenesis in weevils of the tribe Naupactini (Coleoptera, Curculionidae): a Wolbachia-density dependent trait?Marcela Silvina Rodriguero, et al. bioRxiv

PLANT, ROOT AND SOIL MICROBIOME

Preprint: Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens. Maura SRA Silva, et al. bioRxiv

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt. J Yuan, et al. – The ISME Journal

ANIMAL EXPERIMENTS

The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects. CY Lee, et al. – The ISME Journal

TECHNIQUES

Two possible candidate enzymes from Ulva lactuca-associated epiphytic bacteria obtained through PCR and functional evaluation. JS Ruiz-Toquica, et al. – Universitas Scientiarum

WATER AND EXTREMOPHILE MICROBIOME

Genomic insights into the salt tolerance and cold adaptation of Planococcus halotolerans SCU63 T. L Gan, et al. – Archives of Microbiology

PROBIOTICS / PREBIOTICS

The Benefits of Probiotic Interventions in Maternal-Fetal Health: An Appraise Review. P Dhillon, et al. – PharmaNutrition

PHAGES AND VIRUSES

[PDF] Low Host Abundance and High Temperature Determine Switching from Lytic to Lysogenic Cycles in Planktonic Microbial Communities in a Tropical Sea (Red Sea). R Abdulrahman Ashy, et al. – Viruses

June 10, 2020

Greetings from Western New York! This is my first post to Microbiome Digest and I hope it turns out well as I have been busy trying to learn the nuances of publishing on WordPress over the past few months. As a retired Ophthalmologist with a Laboratory Medicine background and research studies in Microbiology I have a distinct affinity for microbiome-related research as it pertains to dysbiosis and pathogenesis. I have included some interesting articles on the association of the microbiome in gallstone disease, gastric and esophageal cancers as well as in HPV cancers. There is also a brief news article pertaining to handwashing of significance in the COVID-19 world we are currently living in. Stay safe and enjoy!

COVID-19

Novel Coronavirus disease 2019 (COVID-19): new challenges and new responsibilities in developing countries. FR Anjum, et al.- Human Vaccines & Immunotherapeutics

APPLIED MICROBIOLOGY

Microplastics provide new microbial niches in aquatic environments. Y Yang, et al.- Applied Microbiology and Biotechnology

GENERAL MICROBIOME

Gallstone Disease and Microbiome. IN Grigor’eva, et al.- Microorganisms

PREGNANCY AND EARLY LIFE

Bacterial Peptidoglycans from Microbiota in Neurodevelopment and Behavior. A Gonzalez-Santana,et al.- Trends in Molecular Medicine

HUMAN SKIN MICROBIOME

News Article: You Need To Use Soap & Sanitizer — But You Also Need To Tend To Your Microbiome

HUMAN GUT MICROBIOME

Comparison of the gut microbiome composition among individuals with acute or long-standing spinal cord injury vs. able-bodied controls. J Li, W Van Der Pol, et al. – The Journal of Spinal Cord …

Influence of microbiota on immunity and immunotherapy for gastric and esophageal cancers. X Zhang, et al.- Gastroenterology Report

ANIMAL MICROBIOME

Exposure of CuO nanoparticles and their metal counterpart leads to change in the gut microbiota and resistome of collembolans. J Ding, et al.- Chemosphere

PLANT, ROOT AND SOIL MICROBIOME

Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching. C Liu, et al- Microorganisms

WATER AND EXTREMOPHILE MICROBIOME

Patterns of environmental variability influence coral‐associated bacterial and algal communities on the Mesoamerican Barrier Reef. L Speare, et al.- Molecular Ecology

PROBIOTICS / PREBIOTICS

Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?. P Pais, et al. – Journal of Fungi

PHAGES AND VIRUSES

Expression and functional study of VpV262 Pol, a moderately halophilic DNA polymerase from the Vibrio parahaemolyticus phage VpV262. Y Gao, et al.- Enzyme and Microbial Technology

Microbiome factors in HPV-driven carcinogenesis and cancers. D Lin, et al.- Plos Pathogens

BIOINFORMATICS

Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. B Tilocca, et al.- Int. J. Mol. Sci