December 10, 2020

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Good morning from New Jersey! Only a few new research articles to share with you today, but FOUR new reviews on the microbiome’s role in cancers and periodontal disease. And if you’re feeling adventurous, PLOS ONE just published an article on human postmortem decomposition that includes a brief evaluation of the buried corpse microbiome.

Jobs

A new postdoctoral position was just posted at the University of Minnesota for research on new methods of fecal microbiota transplantation.

General microbiome

Review – Unexpected guests in the tumor microenvironment: microbiome in cancer, Abigail Wong-Rolle et al., Protein Cell

Review – Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts, Ioannis Fragkioudakis et al., Journal of Medical Microbiology

Human gut microbiome

Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila, Kenny C. Mok et al., mBio

Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes, Wanglong Gou et al., Diabetes Care

Gut microbial ecosystem in Parkinson’s disease: New clinico‐biological insights from multi‐omics, Ai Huey Tan et al., Annals of Neurology

Review – Intervention on Gut Microbiota May Change the Strategy for Management of Colorectal Cancer, Sedigheh Taghinezhad‐S et al., Gastroenterology and Hepatology

Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder, Hiroshi Nishiwaki et al., mSystems

Animal experiments

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization, Soner Yildiz et al., eLife

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice, Niu and Shang et al., Food & Function

A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes, Zhigang Liu et al., mSystems

Plant, root, and soil microbiome

Preprint – Rapid evolution of bacterial mutualism in the plant rhizosphere, Erqin Li et al., bioRxiv

Review – Coffee Microbiota and Its Potential Use in Sustainable Crop Management, Benoit Duong et al., Frontiers in Sustainable Food Systems

Bioinformatics

Review – Tissue-associated microbial detection in cancer using human sequencing data, Rebecca M. Rodriguez et al., BMC Bioinformatics

Techniques

Preprint – BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery, Embriette R. Hyde et al., bioRxiv

December 9, 2020

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In today’s digest read about the selection and microdiversity in glacier-fed streams, Gardnerella vaginalis contribution to the increased rate of group B Streptococcus vaginal colonization, making F1 hybrids in Escherichia coli using MAE (Mass Allelic Exchange), smORFinder (annotation tool to identify small proteins in microbial genomes and metagenomes), and more.
Check out the new Science Friday podcast episode on microbial interactions in cheese rinds and Svetlana’s pick for happy holidays.
Cheers!

Human microbiome

Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver – Holly Lutz – Frontiers in Microbiology

Gut microbiome

Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders – Jian Yang – Science Advances

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome – Dylan G. Maghini – Nature Protocols

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses – Shu Yasuda – iScience

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Fergus Shanahan – Gastroenterology

The gut microbiota is associated with immune cell dynamics in humans – Jonas Schluter
– Nature

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure – Jonel Trebicka – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity – Alexander SF Berry – bioRxiv

Animal experiments

*Gardnerella vaginalis promotes group B Streptococcus vaginal colonization, enabling ascending uteroplacental infection in pregnant mice – Nicole M. Gilbert – American Journal of Obstetrics & Gynecology

Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia – Yue Yu – Biomedicine & Pharmacotherapy

Gut microbiota modulation by both Lactobacillus fermentum MSK 408 and ketogenic diet in a murine model of pentylenetetrazole-induced acute seizure – Ju Young Eor – Epilepsy Research

Host-age prediction from fecal microbiome composition in laboratory mice – Adrian Low – bioRxiv

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor – Aayushi Uberoi – bioRxiv

Water microbiome

*Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome – Stilianos Fodelianakis – bioRxiv

Phages and viruses

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis – Andrey N. Shkoporov – bioRxiv

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase – Marike Palmer – Frontiers in Microbiology

Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics – Suze A. Jansen – Frontiers in Microbiology

Antimicrobial Resistance

Review: Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? – Ana R. Freitas – International Journal of Antimicrobial Agents

Review: Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance – Madangchanok Imchen – Frontiers in Genetics

Predicting clinical resistance prevalence using sewage metagenomic data – Antti Karkman – Communications Biology

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants – John Leech – mSystems

Uncovering hidden antimicrobial resistance patterns within the hospital microbiome – Bastiaan W. Haak and W. Joost Wiersinga – Nature Medicine

Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar – Farah N. Rasool – Journal of Hazardous Materials

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment – Shuyu Jia – Ecotoxicology

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more – Magdalena Skarżyńska – Plos One

Techniques

*Mass allelic exchange: enabling sexual genetics in Escherichia coli – Varnica Khetrapal – bioRxiv

Review: Microbial model communities: To understand complexity, harness the power of simplicity – Johan Bengtsson-Palme – Computational and Structural Biotechnology Journal

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae – Sivkheng Kann – BMC Microbiology

Bioinformatics

*Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes – Matthew G. Durrant and Ami S. Bhatt – Cell Host Microbe

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung – bioRxiv

Species level resolution of female bladder microbiota from marker gene surveys – Carter Hoffman – bioRxiv

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis – Paul E. Smith – Frontiers in Microbiology

Events

H3ABioNet Seminars and Webinars – H3ABioNet Pan African Bioinformatics Network

Inspiring the next generation of scientists… online – The Young Microbiologists Symposium (YMS) 2020

MLCB 2020 Day 1 and 2 talks – Machine Learning in Computational Biology meeting

Podcast

Why We’re Giving Thanks To Microbes For Stinky Cheese with Benjamin Wolfe and Casey Cosetta – Katie Feather and Ira Flatow – Science Friday

Svetlana’s pick

Planning Our “Home-mas” this December – MissPond – Emma Pond

Holiday Gift Guide For Microbe Lovers – Justine Dees – Joyful Microbe

The 2020 cookbook giftlist – Fiona Beckett – Matching Food & Wine

December 08, 2020

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General microbiome

The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy – Mestre & Höfer – Trends in Microbiology

Microbiomes for All – Muth & Caplan – Frontiers in Microbiology

Human oral microbiome

[REVIEW]The Oral Host–Microbial Interactome: An Ecological Chronometer of Health? – Freire, Nelson & Edlund – Trends in Microbiology

Human vaginal microbiome

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism – Cheu et al. – PLOS Pathogens

Human gut microbiome

The Effect of Probiotics Supplementation on Gut Microbiota After Helicobacter pylori Eradication: A Multicenter Randomized Controlled Trial – Tang et al. – Infectious Diseases and Therapy

Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota – Zhao et al. – Pharmacological Research

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries – Tamura & Brumer – Current Opinion in Structural Biology

Animal microbiome (for animals in the wild)

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica – Kim, Cho & Lee – Journal of Microbiology

Plant, root, and soil microbiome

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities – Obayomi et al. – Applied Soil Ecology

Microbes in space

[BOOK CHAPTER]Antarctic Bacteria as Astrobiological Models – Abbott & Pearce – Extremophiles as Astrobiological Models

Bioinformatics

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data – Chen et al. – PLOS One

[REVIEW]Measuring the microbiome: best practices for developing and benchmarking microbiomics methods – Bokulich et al. – Computational and Structural Biotechnology Journal

[REVIEW]Seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks – Desmet et al. – Computational and Structural Biotechnology Journal

Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine – Jahagirdar & Saccenti – Journal of Proteome Research

December 7, 2020

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Today we have some excellent review articles in Science, and Gut as well as several interesting research articles.

COVID-19 

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms – Gordon et al. Science

Robust neutralizing antibodies to SARS-CoV-2 infection persist for months – Wajnberg et al. Science

General Microbiome

[REVIEW] The role of the microbiota in human genetic adaptation – Suzuki and Ley – Science 

Gut microbiome

Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism – Penney et al. mSystems

[REVIEW] Gut microbiota-derived metabolites as central regulators in metabolic disorders – Agus et al. Gut

Human respiratory microbiome

[REVIEW]  Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways. Khanolkar et al. mSystems

Animal microbiome

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen – Gharechahi et al. ISME

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks – Fan et al. BMC Microbiology

Bioinformatics

[REVIEW]  Analysis of microbial compositions: a review of normalization and differential abundance analysis – Lin and Peddada. Npj Biofilms and Microbiomes. 

Non-microbiome pick 

A comparative genomics multitool for scientific discovery and conservation – Zoonomia Consortium. Nature

December 04, 2020

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General microbiome

Highly multiplexed spatial mapping of microbial communities – Shi et al. – Nature

Human respiratory microbiome

Comparison of the human microbiome in adults and children with chronic rhinosinusitis – Park et al. – PLOS One

Human gut microbiome/mycobiome

Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy – Jayasudha et al. – PLOS One

Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes – Matsumoto et al. – Digestion

[REVIEW]The Role of the Gut Microbiota and the Immune System in the Development of Autism – Lungba et al. – Cureus Journal of Medical Science

Animal microbiome

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows – Ekman et al. – PLOS One

Gut microbiota is associated with protection against Marek’s disease virus infection in chickens – Bavananthasivam – Virology

Stingless bees and microbial interactions – de Paula et al. – Current Opinion in Insect Science

Bioinformatics

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis – Hupfauf et al. – PLOS One

December 3, 2020

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A brief digest for today!! Happy reading!!

General microbiome
Polyester microfiber and natural organic matter impact microbial communities, carbon-degraded enzymes, and carbon accumulation in a clayey soil – Guo et al – Journal of Hazardous Materials

Neglected effect of gas atmosphere on hydrogen production in microbial electrolysis cells – Cui et al – Science of The Total Environment

Multi-site human microbiome
A Role for the Microbiota in the Immune Phenotype Alteration Associated with the Induction of Disease Tolerance and Persistent Asymptomatic Infection of Salmonella in the Chicken – Lee et al – Microorganisms

Human gut microbiome
Review: Sleep and Circadian Disruption and the Gut Microbiome-Possible Links to Dysregulated Metabolism – Withrow et al – Current Opinion in Endocrine and Metabolic Research

Plant, root, and soil microbiome
Composition and functional comparison of vetiver root endophytic microbiota originating from different geographic locations that show antagonistic activity towards Fusarium graminearum – Munakata et al – Microbiological Research

Microbiota Diversity Change as Quality Indicator of Soils Exposed to Intensive Periurban Agriculture – Raiger Iustman et al – Current Microbiology

December 02, 2020

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General microbiome

The Interplay of Sex Steroids, the Immune Response, and the Intestinal Microbiota – Pace & Watnick – Trends in Microbiology

[REVIEW]Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome? – Ricci et al. – Int. J. Mol. Sci.

[REVIEW]Microbiota and Obesity: Where Are We Now? – Ballini et al. – Biology

Human vaginal microbiome

Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia – Lee et al. – Diagnostics

Human gut microbiome

A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches – Li et al. – Computational and Structural Biotechnology Journal

[REVIEW]Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives – Vandeputte – Nutrion Reviews

[REVIEW]Harnessing the gut microbiota to promote metabolic health – Zmora – Nutrion Reviews

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Cage bedding modifies metabolic and gut microbiota profiles in mouse studies applying dietary restriction – Gregor et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha) – Mathai et al. – Invertebrate Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks – Wang et al. – Journal of Hazardous Materials

Plant, root, and soil microbiome

Variable characteristics of microbial communities on the surface of sweet cherries under different storage conditions – Zhang et al. – Postharvest Biology and Technology

Biodiversity of pesticides degrading microbial communities and their environmental impact – Kumar et al. – Biocatalysis and Agricultural Biotechnology

Bioinformatics

[REVIEW]Evaluating and minimizing batch effects in metabolomics – Han & Li – Mass Spectrometry Reviews

November 30, 2020

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Hello from Luebeck! Today we selected among others maternal obesity and neurodevelopment, infant growth, breastfeeding and c-section, dental microbiome, gut microbiome and diseases/cancer, a couple of animal and plant microbiome studies. Of particular interest is a study diet and problem solving in a bird species (Parus major).

General microbiome

[REVIEW]The dynamic wound microbiome – Liu et al. – BMC Medicine

[REVIEW]Microbiome and Cervical Cancer – Castanheira et al. – Pathobiology

Pregnancy and early life

[REVIEW]The impact of maternal obesity on childhood neurodevelopment – Tong & Kalish – Journal of Perinatology

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function – Selma-Royo et al. – Microbiome

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life – Guo et al. BMC Pediatrics

Human oral microbiome

Dental plaque microbiota profiles of children with caries-free and caries-active dentition – Qudeimat et al. – Journal of Dentistry

[REVIEW]Microbiomics: Were we all wrong before? – Kumar – Periodontology 2000

[REVIEW]Metaproteome and metabolome of oral microbial communities – Bostanci et al. – Periodontology 2000

Human gut microbiome

Gutmicrobiota, immunity and pain – Santoni, Miccini & Batelli – Immunology Letters

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Shanahan, Ghosh & O’Toole – Gastroenterology

Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus – Wang et al. – Gut Microbes

Animal microbiome (for animals in the wild)

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird – Davidson et al. Scientific Reports

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon – Gillman, McKenney & Lafferty – Scientific Reports

Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life – Reese et al. – Current Biology

Plant, root, and soil microbiome

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream – Piazzon et al. – Microbiome

A comparison of the functional diversity of microbial communities in maize rhizosphere soils in the North West Province of South Africa – Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola – Rhizosphere

[REVIEW]Beyond the extremes: Rocks as ultimate refuge for fungi in drylands – Coleine et al. – Mycologia

Bioinformatics

[REVIEW]Emerging computational tools and models for studying gut microbiota composition and function – Park et al. – Current Opinion in Biotechnology

November 28, 2020

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Greetings from Santiago, Chile! Today, in this brief Digest, we have a preprint with interesting results obtained by the Dutch Microbiome Project. We have as well a couple of papers exploring the relationship between microbiome and COVID-19, and more other papers. Have a nice weekend!

Human and General Microbiome

Preprint: The Dutch Microbiome Project defines factors that shape the healthy gut microbiome – Ranko Gacesa – BioRxiv

Viral Infection-Induced Gut Dysbiosis, Neuroinflammation, and α-Synuclein Aggregation: Updates and Perspectives on COVID-19 and Neurodegenerative Disorders – Cristian Follmer – ACS Chemical Neuroscience

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19 – Taha Baghbani – Microbial Cell Factories

Gut microbiome is more stable in males than in females during the development of colorectal cancer – Haijun Liao – Journal of Applied Microbiology

Expression of toll-like and adhesive receptors on epithelial cells of the oral mucosa in periodontitis – O.A. Lukova – Russian Clinical Laboratory Diagnostics

The Microbiome in Hidradenitis Suppurativa: A Review – Kirsty J. L. Wark – Dermatology and Therapy 

Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes – Meghan H. Shilts – Scientific Reports 

Emotional well-being and gut microbiome profiles by enterotype – Sung-Ha Lee – Scientific Reports 

Vitamin D metabolites and the gut microbiome in older men – Robert L. Thomas – Nature Communications

Animal Microbiome

Reduced rotavirus vaccine efficacy in protein malnourished human-faecal-microbiota-transplanted gnotobiotic pig model is in part attributed to the gut microbiota – V. Srivastava – Beneficial Microbes

Clinical efficacy of spray-based heat-treated lactobacilli in canine atopic dermatitis: a preliminary, open-label, uncontrolled study – Domenico Santoro – Veterinary Dermatology

Extremophiles

Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern – Varun Paul – Scientific Reports 

Microbiome Methods and Analysis

The application potential of machine learning and genomics for understanding natural product diversity, chemistry, and therapeutic translatability – David Prihoda – Natural Product Reports

Other

Efficient protection of microorganisms for delivery to the intestinal tract by cellulose sulphate encapsulation – Walter H. Gunzburg – Microbial Cell Factories

November 27, 2020

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Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications