Enjoy today’s micro-Microbiome Digest!
More microbes
Pre-print: The Pseudomonas aeruginosa LasR quorum-sensing receptor balances ligand selectivity and sensitivity – Amelia R McCready – bioRxiv
Microbes in the news
Living sensor can potentially prevent environmental disasters from fuel spills – Phys.org
Bacteria found in water at Glasgow Royal Hospital for Children – BBC News
Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.
Events and jobs
Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology
Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University
General microbiome
Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports
Human oral microbiome
Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry
Human vaginal microbiome
Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv
Human gut microbiome
Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome
Animal experiments
Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv
Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv
Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition
Animal microbiome
Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express
Water and extremophile microbiome
Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv
Microbes in space
Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv
Phages and viruses
Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science
Bioinformatics
Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv
Techniques
Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome
Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome
Microbes in the news
Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science
Most Viruses And Bacteria Fall From The Sky – Astrobiology Web
Microbes on the market
Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks
Science, career, and publishing
Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv
Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv
The role of saliva in structuring human oral bacterial communities, effects of permafrost thaw on methanogenic communities, and articles on the microbiomes of termites, burying beetles, honey bees, and mosquitoes.
Human oral microbiome
A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow – Diana M Proctor – Nature Communications
Human vaginal microbiome
To ‘douche’ or not to ‘douche’: hygiene habits may have detrimental effects on vaginal microbiota – Erdogan Aslan – Journal of Obstetrics and Gynaecology
Human gut microbiome
Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota – Carolina Serena – The ISME Journal
Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort – Utkarsh Sood – Indian Journal of Microbiology
Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder – Zhi Chen – NeuroReport
Animal experiments
Protective effect of Group B Streptococcus type-III polysaccharide conjugates against maternal colonization, ascending infection and neonatal transmission in rodent models – Emiliano Chiarot – Scientific Reports
Animal microbiome
Pre-print: Axenic Aedes aegypti develop without live bacteria, but exhibit delayed development and reduced oviposition – Maria A Correa – bioRxiv
Two novel strains of Torulaspora delbrueckii isolated from the honey bee gut microbiome and their use in honey fermentation – Joseph P Barry – bioRxiv
Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang – Ecology and Evolution
Rampant Host Switching Shaped the Termite Gut Microbiome – Thomas Bourguignon – Current Biology
Plant, root, and soil microbiome
Melanization of mycorrhizal fungal necromass structures microbial decomposer communities – Christopher W Fernandez – Journal of Ecology
Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence – Andreas Hagenbo – Journal of Ecology
Mycorrhizal symbioses influence the trophic structure of the Serengeti – Bo Maxwell Stevens – Journal of Ecology
The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome – M A Cregger – Microbiome
Water and extremophile microbiome
Pre-print: Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata – Kate Quigley – bioRxiv
Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes – Shiping Wei – Extremophiles
Food microbiology
Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese – Xiaoji Zheng – Food Research International
Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins – Food Research International
Phages and viruses
The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain) – Vicente Pérez-Brocal – PLOS ONE
More microbes
Lactobacillus plantarum lipoteichoic acid inhibits biofilm formation of Streptococcus mutans – Ki Bum Ahn – PLOS ONE
Microbes in the news
In soil-dwelling bacteria, scientists find a new weapon to fight drug-resistant superbugs – Melissa Healy – Los Angeles Times
Interdisciplinary approach yields new insights into human evolution – Liz Entman – Vanderbilt University News
Viruses and Bacteria Travel Along a High-Altitude Superhighway – Dave Roos – Seeker
Science, career, and publishing
Pre-print: The impact on authors and editors of introducing Data Availability Statements at Nature journals – Rebecca Grant – bioRxiv
The gut microbiome of honey bee workers, a review of “Foodomics” approaches to studying digestion and bioactivity, and a new genome sequence for a bacterium isolated from a cell phone screen.
Human gut microbiome
Review: Causal effects of the microbiota on immune-mediated diseases – June L Round – Science Immunology
Possible correlation between gut microbiota and immunity among healthy middle-aged and elderly people in southwest China – Xi Shen – Gut Pathogens
Animal experiments
Pre-print: Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization – Matthew L Jenior – bioRxiv
Pre-print: Microbiota metabolic product deoxycholic acid controls chicken necrotic enteritis – Hong Wang – bioRxiv
Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Science of Food and Agriculture
Animal microbiome
The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science
Bacterial density rather than diversity correlates with hatching success across different avian species – Juan Manuel Peralta-Sánchez – FEMS Microbiology Ecology
Plant, root, and soil microbiome
Influence of metal contamination in soil on metabolic profiles of Miscanthus x giganteus belowground parts and associated bacterial communities – Hoang Nam Pham – Applied Soil Ecology
Pre-print: In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana – Claudia Bartoli – bioRxiv
Effects of Using Arbuscular Mycorrhizal Fungi to Alleviate Drought Stress on the Physiological Traits and Essential Oil Yield of Fennel – Sedigheh Gheisari Zardak – Rhizosphere
Water and extremophile microbiome
Pre-print: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities – Elena Butaitė – bioRxiv
Bacteria from Coral Ecosystem of Kiltan Island, Lakshadweep: Resource for Hydrolytic Enzymes – L Ramlath – International Journal of Cell Science and Biotechnology
Built environment
Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone – Praveen Rahi – International Journal of Systematic and Evolutionary Microbiology
Food microbiology
Review: The role of Foodomics to understand the digestion/bioactivity relationship of food – Grégory Pimentel – Current Opinion in Food Science
Phages and viruses
Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton – Emma J Shelford – Biogeosciences
Small RNA-omics for virome reconstruction and antiviral defense characterization in mixed infections of cultivated Solanum plants – Silvia Turco – Molecular Plant-Microbe Interactions
Metabolomics
UPLC-QTOF-MS metabolomics analysis revealed the contributions of metabolites to the pathogenesis of Rhizoctonia solani strain AG-1-IA – Wenjin Hu – PLOS ONE
Microbes in the news
New imaging technique reveals how dragonfly wings tear bacteria apart – Alayna Hansen – New Atlas
Exploring the microbiome of an ocean bacteria – Kyle Frischkorn – Phys.Org
Microbes on the market
Rebiotix Develops Microbiome Health Index™ to Identify Indicators for Microbiome Restoration – PR Newswire
Bristol-Myers taps Sirenas for ‘global microbiome’ drug discovery – Amirah Al Idrus – FierceBiotech
Givaudan, Unilever target the microbiome – Marc S Reisch – Chemical & Engineering News
Implication of dysbiosis in arthritis in rats, studying soil crust biology and chemistry using metabolomics, a news article on exercise and the microbiome.
Human gut microbiome
Comprehensive analysis of polyamine transport and biosynthesis in the dominant human gut bacteria: Potential presence of novel polyamine metabolism and transport genes – Yuta Sugiyama – The International Journal of Biochemistry & Cell Biology
Animal experiments
Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Tejpal Gill – Arthritis & Rheumatology
Plant, root, and soil microbiome
Linking soil biology and chemistry in biological soil crust using isolate exometabolomics – Tami L Swenson – Nature Communications
Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice – Boknam Jung – Nature Communications
Synergistic action of rhizospheric fungi with Megathyrsus maximus root speeds up hydrocarbon degradation kinetics in oil polluted soil – Michael Dare Asemoloye – Chemosphere
Pre-print: Crop diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – bioRxiv
Microbes in the news
Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us? – Gretchen Reynolds – The New York Times
Bifidobacterium or fiber protect against deterioration of the inner colonic mucus layer – ScienceDaily
Scientists use sound to track tiny organisms in the body – Angela Chen – The Verge
Bacteria and Cancer: Another Connection – Derek Lowe – Science Translational Medicine
Happy New Year from the Microbiome Digest team!
General microbiome
Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv
Human vaginal microbiome
A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology
Human gut microbiome
Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology
Animal microbiome
Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology
Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology
Plant, root, and soil microbiome
Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment
Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil
Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology
Water and extremophile microbiome
Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution
Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv
Food microbiology
Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology
Bioinformatics
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics
Techniques
Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions
Microbes in the news
Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times
Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times
How probiotics can help ward off health complications in premature babies – CTV News
Science, career, and publishing
Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv
Changes to the oral microbiota are associated with risk factors for oral cancer, the benefits of endophytic bacteria on plants, analysis of biofilms from a worldwide sampling of shower hoses.
Pregnancy and early life
Diversity of vaginal microbiota increases by the time of labor onset – Ekaterina Avershina – Scientific Reports
Human oral microbiome
Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer – Daniela Börnigen – Scientific Reports
Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors – Jiyeon Si – Frontiers in Cellular and Infection Microbiology
Animal experiments
Pre-print: Antenatal microbial colonisation of mammalian gut – Elisa Borghi – bioRxiv
Metagenome Analysis of Bodily Microbiota in a Mouse Model of Alzheimer Disease Using Bacteria-derived Membrane Vesicles in Blood – Jin-Young Park – Experimental Neurobiology
Animal microbiome
Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology
Plant, root, and soil microbiome
Pre-print: The ecological genetics of Pseudomonas syringae residing on the kiwifruit leaf surface – Christina Straub – bioRxiv
Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology
Frankia diversity in host-plant root nodules is independent of abundance or relative diversity of Frankia in corresponding rhizosphere soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology
Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere – Muhammad Farhan Ul Haque – Scientific Reports
Rhizodeposition under drought is controlled by root growth rate and rhizosphere water content – Maire Holz – Plant and Soil
Water and extremophile microbiome
Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation – Wei Xie – Environmental Microbiology
Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis – Ramganesh Selvarajan – MicrobiologyOpen
Distribution and phylogeny of anaerobic anammonium-oxidizing (anammox) bacteria in water column of the central Pacific Ocean – Koji Hamasaki – Deap Sea Research Part II: Topical Studies in Oceanography
Built environment
Biofilms in shower hoses – Caitlin R Proctor – Water Research
Phages and viruses
Pre-print: Human Herpes Virus 6 (HHV-6) – Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing – Colin Sharp – bioRxiv
Pre-print: ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages – Chris M Rands – bioRxiv
Bioinformatics
Pre-print: How, when, and where relic DNA biases estimates of microbial diversity – J T Lennon – bioRxiv
Metabolomics
Plasma microbiome-modulated indole- and phenyl-derived metabolites associate with advanced atherosclerosis and postoperative outcomes – Cori A Cason – Journal of Vascular Surgery
Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples – Angela K Boysen – Analytical Chemistry
Techniques
Microfluidics: A new tool for microbial single cell analyses in human microbiome studies – Yuguang Liu – Biomicrofluidics
Pre-print: CLIQ-BID: A method to quantify bacteria-induced damage to eukaryotic cells by automated live-imaging of bright nuclei – Yann Wallez – bioRxiv
Mapping the ecological networks of microbial communities – Yandong Xiao – Nature Communications
More microbes
Pre-print: Molecular insights into Vibrio cholerae’s intra-amoebal host-pathogen interactions – Charles Van der Henst – bioRxiv
Nature to the natural rescue: Silencing microbial chats – Diby Paul – Chemico-Biological Interactions
Microbes in the news
Tracking effects of a food preservative on the gut microbiome – EurekAlert
Microbiome intervention with niacin aids insulin sensitivity – Medical Xpress
Wound scanner shows bacteria glowing if your body is infected – New Scientist
Engineering new cellular scaffolding for bacteria – Celia Henry Arnaud – Chemical & Engineering News
Viruses can transfer genes across the superkingdoms of life – ScienceDaily
Microbes on the market
British Health Technology Company Expanding Into Ten European Countries – PR Newswire
The leaders of ten research universities/institutes pledge to report student and postdoc outcomes in biomedical research as the Coalition for Next Generation Life Science initiative, commensal fungi and their cell-wall mannans can functionally replace benefits of intestinal bacteria, a new cheese starter system with improved bacteriophage resistance and antimicrobial activity.
Events and jobs
Postdoctoral Fellow, Functional Microbiome – Claesen Group, Department of Cellular and Molecular Medicine, Cleveland Clinic (also looking for interested graduate students)
Human nearly-sterile sites
Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation-related genes – Martha Scott Tomlinson – PLOS ONE
Human gut microbiome
Faecal microbiota transplantation for Clostridium difficile infection using a lyophilized inoculum from non-related donors: A case series involving 19 patients – Vigvári Szabolcs – Acta Microbiologica et Immunologica Hungarica
Animal experiments
Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria – Tony T Jiang – Cell Host & Microbe
CCL28-Deficient Mice Have Reduced IgA Antibody–Secreting Cells and an Altered Microbiota in the Colon – Kazuhiko Matsuo – The Journal of Immunology
Animal microbiome
Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid – Hiroki Dan – PLOS ONE
Plant, root, and soil microbiome
Root-derived carbon and nitrogen from beech and ash trees differentially fuel soil animal food webs of deciduous forests – Sarah L Zieger – PLOS ONE
Historical and recent land use affects ecosystem functions in subtropical grasslands in Brazil – Jan L G Leidinger – Ecosphere
Mechanisms of arsenic sequestration by Prosopis juliflora during phytostabilization of metalliferous mine tailings – Corin M Hammond
Transfer Mechanism, Uptake Kinetic Process and Bioavailability of P, Cu, Cd, Pb and Zn in Macrophyte Rhizosphere Using DGT – Shengrui Wang – Environmental Science & Technology
Food microbiology
A Multibacteriocin Cheese Starter System, Comprising Nisin and Lacticin 3147 in Lactococcus lactis, in Combination with Plantaricin from Lactobacillus plantarum – S Mills – Applied and Environmental Microbiology
Bioinformatics
Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data – Marius Vital – mSystems
Discovery of carbamate degrading enzymes by functional metagenomics – Lisa Ufarté – PLOS ONE
Science, career, and publishing
A new data effort to inform career choices in biomedicine – Rebecca Blank – Science
News Feature: The science that’s never been cited – Richard Van Noorden – Nature
Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.
General microbiome
Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology
Pregnancy and early life
Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv
Human gut microbiome
Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health
Animal experiments
Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature
Plant, root, and soil microbiome
Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere
Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology
Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research
Water and extremophile microbiome
Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv
Phages and viruses
Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv
Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications
Bioinformatics
Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv
Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications
Techniques
In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE
More microbes
Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications
Microbes in the news
Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org
What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine
Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle
Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert
Air-eating bacteria found in Antarctica – Cosmos
The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic
Microbes on the market
Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire
Precision Driven Health and Orion Health release Microbiome report – Voxy
Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal
Science, career, and publishing
How to Keep Students in Science – Howard Hughes Medical Institute
An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS
Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv
Editorial: Great mentoring is key for the next generation of scientists – Nature
Amy’s non-microbiology picks
Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science
Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.
Events and jobs
Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark
Human skin microbiome
Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE
Human gut microbiome
Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv
Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology
Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer
Animal experiments
Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology
Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology
Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports
Animal microbiome
Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express
Plant, root, and soil microbiome
Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv
Water and extremophile microbiome
Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science
Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences
Phages and viruses
Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research
Bioinformatics
Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology
More microbes
Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports
Microbes in the news
Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org
Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress
Microbe threat to Mars – Andrew Masterson – Cosmos
Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist
Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health
CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News
Bacteria hysteria
Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee
Science, career, and publishing
Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv
Microbiome Digest - Bik's Picks 