August 23, 2019

Good morning everyone!

This post is written from lovely NYC, quite a distance from my hometown in Israel. If you’re working on microbial ecology in the city and care for a cup of coffee (on me!) and a rather interesting chat about science, entreprenurship and agriculture- please contact me via barakdror@outlook.com or just find me on Linkedin.

Today post will feature highly recommended podcast, a great antimicrobial resistance review paper, Cocaine effect on gut microbiota, some cool bioinformatics tools papers, fascinating animal microbiome studies and more.

Resources and Podcast

I’m a huge fan of the This Week in Microbiology podcast. On their 201 episode the team hosted Prof. Mark Martin (U of Puget Sound) with some great list of papers for 1st year undergrads- but it is a great opportunity to read about general concepts and direction in micrboiology. I truely enjoed both the episode and the recommended papers.

15 Biotech-Themed Online Courses to Try at Home

Antibiotic Resistance

Defining and combating antibiotic resistance from One Health and Global Health perspectives, Sara Hernando-Amado, Nature Microbiology

Bioinformatics

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data, Chenhao Li, Microbiome

Analysing complex metagenomic data with MicroWineBar, Franziska Klincke ,bioRxiv

A systematic NGS-based approach for contaminant detection and functional inference, Sung-Joon Park, bioRxiv

Human and Animal microbiome

Cocaine Induces Inflammatory Gut Milieu by Compromising the Mucosal Barrier Integrity and Altering the Gut Microbiota Colonization, Ernest T. Chivero, Scientific Reports

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review, Narjis Kraimi, Physiology & Behavior

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system, Yaron Krotman, bioRxiv

Non‐random associations of maternally transmitted symbionts in insects: The roles of drift versus biased co‐transmission and selection, Hugo Mathe-Hubert, Molecular Ecology

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant, G. Minard, Environmental Microbiology

Food microbiome

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities, Xiaoqing Tan, Microbiome

Environmental microbiome

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome, Pedro J. Cabello-Yeves, Microbiome

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica, Emma Martinez-Alonso, Scientific Reports

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August 19, 2019

Monday’s digest is about microbiota as biomarker in diverse human diseases such as alopecia areata and bladder cancer, how arabinoxylan and grape pomace affects microbiota in rodents and microbial characterization of multi-strain probiotic VSL3 .

General microbiome

What Pediatricians Should Know Before Studying Gut Microbiota – Lorenzo Drago – Journal of Clinical Medicine

The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Human microbiome

The sex-specific interaction of the microbiome in neurodegenerative diseases – Laura M. Cox – Brain Research

Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers – Oscar M. Moreno-Arrenos – Journal of the European Academy of Dermatology and Venereology

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment – Rui Zhao – Oral Diseases

Urinary microbiota – a potential biomarker and therapeutic target for bladder cancer – Hai Bi – Journal of Medical Microbiology

Animal experiments

Effect of arabinoxylan on colonic bacterial metabolites and mucosal barrier in high‐fat diet‐induced rats – Shanshan Li – Food Science and Nutrition

The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes – Xiaokang Lv – BioRxiv

Effects of grape pomace and seed polyphenol extracts on the recovery of gut microbiota after antibiotic treatment in high‐fat diet‐fed mice – Feng Lu – Food Science and Nutrition

Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development – Juliette Mouries – Journal of Hepatology

Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows – Yuliaxis Ramayo‐Caldas – Journal of Animal Breeding and Genetics

The gastrointestinal fate of limonin and its effect on gut microbiota in mice – Min Gu – Food and Function

Plant, root, soil microbiome

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

Salinity-induced changes in the rhizosphere microbiome improve salt tolerance of Hibiscus hamabo – Yongge Yuan – Plant and Soil

Water and extremophile microbiome

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California – Brittany J. Suttner – BioRxiv

Probiotics

Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3 – Diego Mora – Microbial Biotechnology

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota – Yasuhiro Koga – BMJ Open Gastroenterology

Non Microbiology Picks

First cells may have emerged because building blocks of proteins stabilized membranes – Science Daily

August 15, 2019

Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

August 13, 2019

Have a good Tuesday!  Today we have a brief digest, covering papers about Staphylococcus and Skin infections and the gut microbiome and Insomnia disorder, in addition with different studies in mice and a report showing genetic relationships between plants and bacterial community configuration. 

 

Human or General Microbiome

Review: Protective effect of the “food-microorganism-SCFAs” axis on colorectal cancer: from basic research to practical application – Han Shuwen – Journal of Cancer Research and Clinical Oncology

Strains of Staphylococcus aureus that Colonize and Infect Skin Harbor Mutations in Metabolic Genes – Karen P. Acker – IScience

Inflamm-aging micrornas may integrate signals from food and gut microbiota by modulating common signalling pathways – Laura Teodori – Mechanisms of Ageing and Development

Gut Microbiota as a Subjective Measurement for Auxiliary Diagnosis of Insomnia Disorder – Bingdong Liu – Frontiers in Microbiology

 

Animal Microbiome

Adhesive Bifidobacterium Induced Changes in Cecal Microbiome Alleviated Constipation in Mice – Linlin Wang – Frontiers in Microbiology

Short-term dietary restriction in old mice rejuvenates the aging-induced structural imbalance of gut microbiota – Ting Zeng – Biogerontology

Species-specific effects of arsenic on the soil collembolan gut microbiota – Yi-Fei Wang – Ecotoxicology and Environmental Safety

Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill – Ruiqun Chen – Journal of Ethnopharmacology

Age- and diet-specific effects of chronic exposure to chlorpyrifos on hormones, inflammation and gut microbiota in rats – Jin-Wang Li – Pesticide Biochemistry and Physiology

High-throughput 16S rRNA gene sequencing reveals that 6-hydroxydopamine affects gut microbial environment – Jin Gyu Choi – PLoS ONE

 

Plant Microbiome

Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization – Rafael Soares Correa de Souza – Frontiers in Microbiology

 

Non-Microbiology Picks

Science–graphic art partnerships to increase research impact – Colin K. Khoury – Communications Biology

August 3, 2019

Have a happy weekend! Today, in this Digest: an interesting study of the human placenta microbiome, papers showing associations between microbiome and pancreatic or lung cancer, and an update of the pathogenesis of bacterial vaginosis. In addition, a paper showing that the microbiome in primates has a different evolutionary pattern in comparison with the host.  Enjoy!

 

Human and General Microbiome

Human placenta has no microbiome but can contain potential pathogens – Marcus C. de Goffau – Nature

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer – Roberto Mendez – Carcinogenesis

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints – Andres Gomez – mSphere

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules – Yijiu Ren – Translational Lung Cancer Research

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis – Christina A Muzny – The Journal of Infectious Diseases

Review: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health – Aimeé Parker – Gut Microbes

Editorial: The only thing that stops a bad microbiome, is a good microbiome – Jessica R. Galloway-Peña – Haematologica

Review: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation – Andrew J. McBain – Clinical Microbiology Reviews

News: Microbiome therapeutics go small molecule – Megan Cully – Nature Reviews Drug Discovery

Pharmacomicrobiomics informs clinical pharmacogenomics – Theodora Katsila – Future Medicine

Each Additional Day of Antibiotics is Associated with Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients – Ashley M Rooney, BSc – Clinical Infectious Diseases

Prevention and treatment of recurrent Clostridioides difficile infection – Jae Shin – Current Opinion in Infectious Diseases

An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia – Wenkui Dai – Gigascience

Review: Connection between gut microbiome and the development of obesity – Cuiting Zhi – European Journal of Clinical Microbiology & Infectious Diseases

Animal Microbiome

Hyperuricemia is associated with impaired intestinal permeability in mice – Daxing Xu – Gastrointestinal and Liver Physiology

 

Beneficial compounds and Foods

Prevention of Vascular Inflammation by Pterostilbene via Trimethylamine-N-Oxide Reduction and Mechanism of Microbiota Regulation – Yen‐Chun Koh – Molecular Nutrition and Food Research

Interactions of tea polyphenols with intestinal microbiota and their implication for cellular signal conditioning mechanism – Yongyong Li – Journal of Food Biochemistry

Hass Avocado Inclusion in a Weight-Loss Diet Supported Weight Loss and Altered Gut Microbiota: A 12-Week Randomized, Parallel-Controlled Trial – Susanne M Henning – Current Developments in Nutrition

 

Plant Microbiome

Host plant-dependent effects of microbes and phytochemistry on the insect immune response – Su’ad A. Yoon – Oecologia

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria – Barney A. Geddes – Nature Communications 

August 1, 2019

Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv

July 27, 2019

Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology