Another day of a short digest. Enjoy the beautiful pictures demonstrating the use of bacteria in art!
ASM Microbe 2017, June 1-5th in New Orleans
BioSharing: Harnessing Metadata Standards For The Data Commons – Susanna-Assunta Sansone – BioRXiv
Researchers Create Color Images With Bacteria
Scientists teach E.coli bacteria to ‘draw’. Bacteria draws Mario
Today’s digest includes great reviews on plant-microbe interactions and microbial individual-based ecology (μIBEd). Lastly, a paper looking at approaches to understanding phage niches.
General Microbiome and Microbiology
Bacterial colonization and succession in a newly opened hospital. Lax S. Science Translational Medicine
Human gut microbiome
Review: Gut microbiota and host defense in critical illness. Jacobs MC. Correct Opinions in Critical Care
Microbiota-gut-brain axis and the central nervous system. Zhu X. Oncotarget
Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding. Ilhan ZE. ISME Journal
Gut Microbiota: Potential for a Unifying Hypothesis for Prevention and Treatment of Hypertension. Qi Y. Circulation Research
Human microbiome and immune system
Cerebrovascular malformations: Microbiota promotes cerebral cavernous malformations. Ridler C. Nature Review Neurology
Microbiota in T-cell homeostasis and inflammatory diseases. Lee N. Experimental and Molecular Medicine
Microbiota modulation counteracts Alzheimer’s disease progression influencing neuronal proteolysis and gut hormones plasma levels. Bonfili L. Scientific Reports
Animal and insect microbiome
Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains. Jordan HR. Insects
Microbiome modelling
Review: Advancing microbial sciences by individual-based modelling. Hellweger FL. Nature Reviews Microbiology
Plant, soil, and air microbiome
Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region. Wu W. Science of the Total Environment
Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA. Edwardson CF. ISME Journal
Review: Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. Martin FM. Science
Review: Dimensions of biodiversity in the Earth mycobiome.Peay GY. Nature Reviews Microbiology
Experimental soil warming shifts the fungal community composition at the alpine treeline. Solly EF. New Phytologist
Virology
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Hayes S. Virus
Bacteriophage transfer during faecal microbiota transplantation in <i>Clostridium difficile</i> infection is associated with treatment outcome. Zuo T. Gut Microbiota
Non-pylori Helicobacters (NHPHs) induce shifts in gastric microbiota in Helicobacter pylori-infected patients – Peng et al. – Frontiers in Microbiology
Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population – Koliada et al. – BMC Microbiology
The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Young Lim et al. – Gut (BMJ)
Fungal microbiota dysbiosis in IBD – Sokol et al. – Gut (BMJ)
A tale of two risks: smoking, diabetes and the subgingival microbiome – Ganesan et al. – The ISME Journal
The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate – Popova et al. – Frontiers in Microbiology
Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? – Tidjani Alou et al – Frontiers in Microbiology
Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938 – Grande et al. – Frontiers in Microbiology
Review: Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling – Yang et al. – Cellular Physiology and Biochemistry
A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria – Flórez et al. – Frontiers in Microbiology
Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Bonham et al. – BioRxiv
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access – Taboada et al. – Frontiers in Microbiology
In vitro assessment of Pediococcus acidilactici Kp10 for its potential use in the food industry – Abbasiliasi et al. – BMC Microbiology
In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment – Allegretta et al. – Frontiers in Microbiology
Metabolic anticipation in Mycobacterium tuberculosis – Eoh et al. – Nature Microbiology
Predicting Drug Resistance Evolution: Antimicrobial Peptides Vs. Antibiotics – Yi et al. – BioRxiv
Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al. – BioRxiv
Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean – Frischkorn et al. – The ISME Journal
BSocial: Deciphering Social Behaviors within Mixed Microbial Populations – Purswani et al. – Frontiers in Microbiology
A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination – Collins and Didelot – BioRxiv
Association Mapping From Sequencing Reads Using K-mers – Rahman et al. – BioRxiv
MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes – Pericard et al. – BioRxiv
Perspective: Our path to better science in less time using open data science tools – Stewart Lowndes et al. – Nature Ecology & Evolution
Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance – Mead et al. – PLoS Biology
Review: Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure – Siliakus et al. – Extremophiles
Exploring a possible link between the intestinal microbiota and feed efficiency in pigs
Ursula M. McCormack et al., Applied and Environmental Microbiology
Modulation of the Gut Microbiota by Krill Oil in Mice Fed a High-Sugar High-Fat Diet
Chenyang Lu et al., Frontiers in Microbiology
Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?
Eamonn M. M. Quigley, Nature Reviews Gastroenterology & Hepatology (Online since March 30, 2017; however this has not been pointed out here before)
Mini review: The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens
Rute G. Matos et al., Frontiers in Microbiology
Dafne Pérez-Montarelo et al., Frontiers in Microbiology
Stéphanie Bouillot et al., Scientific Reports (Nature)
Intrinsic Toxin-Derived Peptides Destabilize and Inactivate Clostridium difficile TcdB
Jason L. Larabee et al., mBio
Vaginal Lactobacillus Inhibits HIV-1 Replication in Human Tissues Ex Vivo
Rogers A. Ñahui Palomino et al., Frontiers in Microbiology
Assessing the Risk of Probiotic Dietary Supplements in the Context of Antibiotic Resistance
Min Zheng et al., Frontiers in Microbiology
Daniel M. Linares et al., Frontiers in Microbiology
Letícia de C. Oliveira et al., Frontiers in Microbiology
Health benefit of vegetable/fruit juice-based diet: Role of microbiome
Susanne M. Henning et al., Scientific Reports (Nature)
Rizwana Parveen Rani et al., Frontiers in Microbiology
Stefan Bereswill et al., Scientific Reports (Nature)
News and Views: Paediatrics: Are human milk oligosaccharides the magic bullet for necrotizing enterocolitis?
Michael S. Caplan, Nature Reviews Gastroenterology & Hepatology
Francisco Rodríguez-Gómez et al., Frontiers in Microbiology
A broad-spectrum bactericidal lipopeptide with anti-biofilm properties
Ohad Meir et al., Scientific Reports (Nature)
The anticancer peptide TAT-RasGAP317-326 exerts broad antimicrobial activity
Mathieu Heulot et al., Frontiers in Microbiology
Sang Woo Seo et al., Scientific Reports (Nature)
High-Definition Electronic Genome Maps From Single Molecule Data
John S. Oliver et al., BioRxiv
Ben Pascoe et al., PeerJ (not peer reviewed)
Feature: Mining microbes: Creating genomic tools to fight disease
Amber Dance, Science
Yang Zhou et al., Frontiers in Microbiology
Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development
Stephanie Turner et al., Frontiers in Microbiology
Ramon Terrado et al., The ISME Journal
Hypothesis & Theory: The hyperarid core of the Atacama Desert, an extremely dry and carbon deprived habitat of potential interest for the field of carbon science
Armando Azua-Bustos et al., Frontiers in Microbiology
Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides
Shaun Stairs et al., Nature Communications
Virus origin could relate to the act of prey among primitive life forms
Eslam Abbas, PeerJ (not peer reviewed)
Kavitha Reddy, PeerJ (not peer reviewed)
Feature: Introducing ORCID
John Bohannon and Kirk Doran, Science
Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans. Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)
Events and jobs
* Scientist – Microbiomics – ZymoResearch
PhD in microbiology – Université Catholique de Louvain (UCL)
Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT
General microbiome
* Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal
* Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE
Pregnancy and early life
PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes
The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.
Human oral microbiome
The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity
Human gut microbiome
Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN
The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience
The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress
* Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection
Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig
Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery
* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America
Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology
Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.
Animal experiments
* Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology
Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation
Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science
The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry
Animal microbiome
The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE
The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research
Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology
This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth-Microbiota Interactions in Veterinary Species – Peachey LE – Trends in Parasitology
Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME
Plant, root, and soil microbiome
Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal
Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments
Water and extremophile microbiome
Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal
A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin
The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin
The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin
Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management
Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data
Built environment (subways, indoor surfaces)
Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen
Probiotics / prebiotics
Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms
Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors
Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology
Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition
Bioinformatics
PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv
Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE
Techniques
Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews
Microbes in the news
Cork scientists link gut bacteria to anxiety disorders
New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness
Optical nanofiber ‘hears’ bacteria swim, cancer cells move
Microbes on the market
* BiomX raises $24 million to boost bacteria based drugs
Ed’s non-microbiology picks
Breakthrough in delirium research ‘solves 2,500-year-old mystery’
Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine
High levels of exercise linked to nine years of less aging (at the cellular level)
Migratory birds bumped off schedule as climate change shifts spring
PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members – Megan S. Patterson – Human Kinetics
Edible insects could play key role in cutting harmful emissions – EurkAlert!
Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.
General microbiome
Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE
Human oral microbiome
The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv
Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ
Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research
Human gut microbiome
Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis
Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens
Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology
Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology
Animal experiments
* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature
* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS
Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research
Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports
Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports
Animal microbiome
* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe
The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications
Plant, root, and soil microbiome
Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments
High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research
Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE
Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology
Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry
The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology
Water and extremophile microbiome
Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews
Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv
Probiotics/prebiotics
Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology
Bioinformatics
dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics
Techniques
Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine
Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology
Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE
More microbes
When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology
Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology
Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications
Microbes in the news
Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News
A defence mechanism that can trap and kill TB bacteria – Science Daily
Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek
Bacteria art
Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com
Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.
Human gut microbiome
Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv
Ocean, river, and stream microbiome
Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography
Bacterial biogeography across the Amazon river-ocean continuum Doherty M. Frontiers in Microbiology
Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay. Yu SX. Marine Pollution Bulletin
The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology
The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology
Plant, soil, and air microbiome
Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine
Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal
Animal gut microbiome
Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science
Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science
Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution
Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One
Biotechnology
Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology
Antibiotic
Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal
Extreme environment
Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances
Faecal microbiome
pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere
Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal
Microbes in the news
Southern California beaches get bacteria warnings after rain
Monterey County Herald
Bustle
An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.
Human oral microbiome
The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv
Human gut microbiome
* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology
Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology
Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports
Animal experiments
Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition
Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome
Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut
Animal microbiome
Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology
Plant, root, and soil microbiome
Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology
Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact
Water and extremophile microbiome
The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal
Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography
Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution
Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology
Probiotics/prebiotics
Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology
Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ
Bioinformatics
Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports
Techniques
Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research
* Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology
Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research
More microbes
Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution
Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology
Microbes in the news
Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News
Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert
Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline
Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress
Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas
Microbes on the market
Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire
Bacteria and art
This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia
Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu
Amy’s non-microbiology picks
Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature
General Microbiome
Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology
Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology
Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments – Matthew L Jenior – BioRxiv
Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods
Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods
Pathogens
Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology
A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology
Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology
Environmental Microbiology
Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv
Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology
Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv
Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology
Genomics
Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology
Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution
Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv
Evolution
Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution – Joanna M. Wolfe – BioRxiv
Bioinformatics
AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)
TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)
Other
Preprinting Microbiology – Patrick D Schloss – BioRxiv
Non – Microbiology picks
News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)
Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano – Nature
The Microbiome – The Biochemist (full issue)
*Review: What fertility specialists should know about the vaginal microbiome: a review – Juan Antonio García-Velascoa – Reproductive BioMedicine Online
Microbiota-Induced Antibodies Are Essential for Host Inflammatory Responsiveness to Sterile and Infectious Stimuli – Daniel Cisalpino – Journal of Immunology
Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans – Timothy A. Scott – Cell
Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell
Examining the role of the microbiome in the effectiveness of colorectal cancer treatment – Jim Fessenden – UMass Medical School Communications
Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science
Infant mice lack microbes that help fight intestinal infection – EurekAlert!
Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation – Linlin Wang – Food & Function
Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet – Yue Shang – Lipids
Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature – Andrian P. Gajigan – Microbiology Open
Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi) – Jun Chen – AMB Express
*Opinion: Mammary microbiota of dairy ruminants: fact or fiction? – Pascal Rainard – Veterinary Research
Determination of the microbial community features of Haemaphysalis flava in different developmental stages by high-throughput sequencing – Deyong Duan – Journal of Basic Microbiology
A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease – Britt Koskella – New Phytologist
Soil aggregates as massively concurrent evolutionary incubators – Matthias C Rillig – ISME
Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment – Qing Wang – Biology and Fertility of Soils
*Editorial: Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont – Donald L. Smith – Frontiers in Plant Science
Warming enhances old organic carbon decomposition through altering functional microbial communities – Lei Cheng – ISME
Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology
Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil – Xuesong Luo – Journal of Basic Microbiology
Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic – Mattias L. Johansson – Diversity and Distributions
Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – Inga Leena Angell – Letters in Applied Microbiology
*Review: The life sulfuric: Microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports
Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra – Enrique Zozaya-Valdés – Environmental Microbiology
Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds – Christian Wurzbacher – ISME
Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy
A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data – Yuanyuan Ma – Preprints
Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline – Daniel J. White – Journal of Computational Biology
Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell
‘Genetic scalpel’ can manipulate the microbiome, Yale study shows – Bill Hathaway – Yale News
What is broad-range 16S rDNA PCR? – Amani Patel – Microbiology and Infectious Disease
Microbiome: The Body’s Great Conductor – Conan Milner – Epoch Times
Our Gut Microbes Have Circadian Rhythms, Too — And They Might Own Us – Jesslyn Shields – HowStuffWorks
The Bacteria That Can Help Find Land Mines – Daniel Akst – The Wall Street Journal
Grant Addresses Computational Challenges in Microbiome Research – Jacobs School of Medicine and Biomedical Science
Microbiome Digest - Bik's Picks 