November 7, 2022

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

July 15, 2020

Posted on July 15, 2020 by crallenblevins

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 3^rd 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

September 3, 2019

Posted on September 3, 2019 by Alyson

Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

November 29, 2018

Posted on November 29, 2018 by Tulika Arora

Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice – Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

November 10, 2018

Posted on November 10, 2018 by JP Cardenas

Human and General Microbiome

Review: Clinical Application and Potential of Fecal Microbiota Transplantation – R.E. Ooijevaar – Annual Review of Medicine

Editorial: A novel treatment for patients with constipation: Dawn of a new age for translational microbiome research? – Ayesha Shah – Indian Journal of Gastroenterology

Research Highlight: Of ethnicity, environment, and microbiota – Sundararajan Jayaraman – Cellular & Molecular Immunology

Minireview: Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder – Rachael Horne – Frontiers in Psychiatry

Case Report: Hirschsprung’s Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome – Georg Singer – Case Reports in Pediatrics

News and Views: Rules of engagement in the gut microbiome – Elze Rackaityte – Nature Medicine

Preview: When Soluble Fibers Meet Hepatocellular Carcinoma: The Dark Side of Fermentation – Suchira Gallage – Cell Metabolism

Preview: A Microbiota Assimilation – Justin Sonnenburg – Cell Metabolism

Fecal microbiota transplantation: restoring the injured microbiome after allogeneic hematopoietic cell transplantation – Zachariah DeFilipp – Biology of Blood and Marrow Transplantation

Studies of nonhuman primates: key sources of data on zoonoses and microbiota – B.Davoust – New Microbes and New Infections

Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition – Cristian Pasquaretta – Genes

Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans – Jennifer R. Bratburd – mBio

A randomized double-blind placebo-controlled trial showing rifaximin to improve constipation by reducing methane production and accelerating colon transit: A pilot study – Uday C. Ghoshal – Indian Journal of Gastroenterology

Zinc Deficiency and the Recurrence of Clostridium difficile Infection after Fecal Microbiota Transplant: A Retrospective Cohort Study – Blake A. Niccum – Journal of Nutrition and Metabolism

Recurrent Clostridium difficile Infection: Risk Factors, Treatment, and Prevention – Jung Hoon Song – Gut and Liver

Profiles and Perspectives: Mitochondrial dysfunction and gut microbiota imbalance: An intriguing relationship in chronic kidney disease – Denise Mafra – Mitochondrion

Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population – Filipa Godoy-Vitorino – Frontiers in Microbiology

Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels – Mary Rodríguez-Rabassa – International Journal of Environmental Research and Public Health

Minireview: Human bacterial repertoire of the urinary tract: a potential paradigm shift – Aurélie Morand – Journal of Clinical Microbiology

Review: Role of gut microbiota in intestinal wound healing and barrier function – Ashfaqul Alam – Tissue Barriers

Initial microbial community of the neonatal stomach immediately after birth – Sarah Bajorek – Gut Microbes

The Role of Diet, Micronutrients and the Gut Microbiota in Age-Related Macular Degeneration: New Perspectives from the Gut⁻Retina Axis – Emanuele Rinninella – Nutrients

Review: Candida Interactions with the Oral Bacterial Microbiota – Daniel Montelongo-Jauregui – Journal of Fungi

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants – Elena Biagi – Frontiers in Microbiology

First Insights into the Gut Microbiota of Mexican Patients with Celiac Disease and Non-Celiac Gluten Sensitivity – Jose F. Garcia-Mazcorro – Nutrients

Dietary Exposure to the Environmental Chemical, PFOS on the Diversity of Gut Microbiota, Associated With the Development of Metabolic Syndrome – Keng Po Lai – Frontiers in Microbiology

Death Microbiome

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue – Whitney A. Kodama – Journal of Forensic Sciences

Animal Microbiome / Animal Experiments

Review: Chicken Gut Microbiota: Importance and Detection Technology – Yue Shang – Frontiers in Veterinary Sciences

Predator odor exposure in early adolescence influences the effects of the bacterial product, propionic acid, on anxiety, sensorimotor gating, and acoustic startle response in male rats in later adolescence and adulthood – Deanne Tak On Wah – Physiology & Behavior

Pharmacological Activation of PXR and CAR Down-regulates Distinct Bile Acid-metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis – Joseph L Dempsey – Toxicological Sciences

Protective effects of ghrelin on fasting-induced muscle atrophy in aging mice – Chia-Shan Wu – The Journals of Gerontology: Series A

The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice – Bei Gao – Chemical Research in Toxicology

Differential effects of coconut versus soy oil on gut microbiota composition and predicted metabolic function in adult mice – Vania Patrone – BMC Genomics

Pharmaceutical Impact of Houttuynia Cordata and Metformin Combination on High-Fat-Diet-Induced Metabolic Disorders: Link to Intestinal Microbiota and Metabolic Endotoxemia – Jing-Hua Wang – Frontiers in Endocrinology

Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice – Umesh D. Wankhade – Scientific Reports

Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice – Naoki Sasaki – Frontiers in Microbiology

Effect of Grifola frondosa 95% ethanol extract on lipid metabolism and gut microbiota composition in high-fat diet-fed rats – Yu-Yang Pan – Food & Function

Reduction in butyrate-producing Lachnospiraceae contributes to stress-induced visceral hypersensitivity in rats – Jindong Zhang – Journal of Gastroenterology and Hepatology

Beneficial Compounds and Probiotics

Review: Potential Prebiotic Properties of Nuts and Edible Seeds and Their Relationship to Obesity – Clara S. A. Sugizaki – Nutrients

Review: Resveratrol, Metabolic Syndrome, and Gut Microbiota – Alice Chaplin – Nutrients

Isolation and Characterization of Potentially Probiotic Bacterial Strains from Mice: Proof of Concept for Personalized Probiotics – Larissa S. Celiberto – Nutrients

Two alkaline motifs in the Lactobacillus salivarius Lv72 OppA surface are important to its adhesin function – C. Martín – Beneficial Microbes

Protocols

Book Chapter: Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology

Bioinformatics

Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome – Huiru Zheng – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Food and Nutritional Microbiome

Microbiomes Associated With Foods From Plant and Animal Sources – Karen G. Jarvis – Frontiers in Microbiology

Fecal microbiota responses to bran particles are specific to cereal type and in vitro digestion methods that mimic upper gastrointestinal tract passage – Yunus Emre Tuncil – Journal of Agricultural and Food Chemistry

Gut carbohydrate inhibits GIP secretion via a microbiota/SCFA/FFAR3 pathway – : Eun-Young Lee – Journal of Endocrinology

Review: Human Breast Milk Bacteriome in Health and Disease – Anna Ojo-Okunola – Nutrients

Relative Validity and Reproducibility of a Food Frequency Questionnaire to Assess Nutrients and Food Groups of Relevance to the Gut Microbiota in Young Children – Claudia Leong – Nutrients

Other

Surface Exposure and Packing of Lipoproteins into Outer Membrane Vesicles Are Coupled Processes in Bacteroides – Ezequiel Valguarnera – mSphere

The Transferable Resistome of Produce – Khald Blau – mBio

17 October, 2018

Posted on October 17, 2018 by Itumeleng

General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

September 17, 2018

Posted on September 17, 2018 by Alyson

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnostics The impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

July 30, 2018

Posted on July 29, 2018 by Svetlana Ugarcina Perovic

Today’s digest features the microbiomes of a XVIII century mummy (Krásna Hôrka, Slovakia), an interesting initiative out of Belgium (Disbiome, a database of microbiota-disease associations), exciting news from Kamagata lab about improved culturing of environmental samples, promising findings on gut bacteria byproduct that protects against Salmonella, and much more. Happy reading!

Human microbiome

*Disbiome database: linking the microbiome to disease – Yorick Janssens – BMC Microbiol.

*The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment – Lucia Kraková – Environ Microbiol.

Gut microbiome

*A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection – Amanda Jacobson – Cell Host & Microbe

Simulation and modeling of dietary changes in the infant gut microbiome – Daniel Medina – FEMS Microbiol Ecol.

Human gut bacteria as potent class I histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid – Samantha Yuille – PLoS One

Review: An update on the role of gut microbiota in chronic inflammatory diseases, and potential therapeutic targets – Bobbi Laing – Expert Rev Gastroenterol Hepatol.

A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode – Annamaria Painold – Bipolar Disord.

Review: The Gut-Brain Axis, the Human Gut Microbiota and Their Integration in the Development of Obesity – Edward Bliss – Front Physiol.

Fungal dysbiosis in cirrhosis – Jasmohan S Bajaj – Hepatology

Urinary tract microbiome

The bacterial microbiota in first-void urine from men with and without idiopathic urethritis – Maria Frølund – PLoS One

Lung microbiome

Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients – Xiaoling Qi – Respir Res.

Plant microbiome

Bacterial community assemblages in the rhizosphere soil, root endosphere and cyst of soybean cyst nematode-suppressive soil challenged with nematodes – Muzammil Hussain – FEMS Microbiology Ecology

Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system – Yanglei Yi – Environ Microbiol.

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling – Garcia Joshua – Front Microbiol.

Water microbiome

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater – Roland Wilhelm – Environ Microbiol.

Techniques

*Isolation of Previously Uncultured Slow-growing Bacteria by Using a Simple Modification in Preparation of Agar Media – Souichiro Kato – Applied and Environmental Microbiology

Review: The role of the gut microbiota on animal model reproducibility – Patricia Turner – Animal Model Exp.

Review: Environmental enrichment and mouse models: Current perspectives – Kathryn Bayn – Animal Model Exp.

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – J Vis Exp.

Bioprinting microbial communities to examine interspecies interactions in
time and space – William Frederick Hynes – Biomed. Phys. Eng. Express

January 19, 2018

Posted on January 19, 2018 by Anitha Isaiah

Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology