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
Quite short Microbiome Digest today with plastic degrading microbes in news, while highlighted paper is about engineered bacteria. Enjoy your reading!
Events and jobs
Bioinformatics Research Associate, JDRF bioinformatics center, Harvard
General microbiome
Effect of meteorological factors and geographic location on methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci colonization in the US – Natalia Blanco – PLOS One
Surface-attached molecules control Staphylococcus aureus quorum sensing and biofilm development – Minyoung Kevin Kim – Nature Microbiology
Human respiratory microbiome
A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer – Simon J. S. Cameron – PLOS One
Human gut microbiome
Review: Screening and treating Helicobacter pylori infection for gastric cancer prevention on the population level – Yi-Chia Lee – Journal of Gastroenterology and Hepatology
Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen – Gianluigi Zaza – PLOS One
Animal microbiome
The microbiota of diapause: how host-microbe associations are formed after dormancy in an aquatic crustacean – Alexandra A. Mushegian – Animal Ecology
Water and extremophile microbiome
The Variable Influence of Dispersant on Degradation of Oil Hydrocarbons in Subarctic Deep-Sea Sediments at Low Temperatures (0–5°C) – Robert M. W. Ferguson – Scientific Reports
Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA – Christian F Edwardson – ISME Journal
Microbial biotechnology
Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation – David T Riglar – Nature Biotechnology
Microbes in space
Traces of Barents Sea plankton, bacteria from Madagascar found on ISS surface
Techniques
ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data – Yuttachon Promworn – PLOS One
ANNOgesic: A Pipeline To Translate Bacterial/Archaeal RNA-Seq Data Into High-Resolution Genome Annotations – Sung-Huan Yu – bioRxiv
Microbes in the news
Super-Charged Antibiotic Could Stop Resistant Bacteria For Years
Newly-Evolved Microbes Could Be Eating 90% of Ocean Plastic
Dirt has a microbiome, and it may double as an antidepressant
Microbes in art
A bit of a late night Digest today! Still here though, quite a few articles about rhizosphere, a hot topic at the moment; some genome sequences from ASM Genome Announcements, and a few methods & bioinformatics papers. Enjoy!
Multi-site human microbiome
Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China
Shiao-Wen Li et al. – Frontiers in Microbiology
Review: Recent advances in dental biofilm: impacts of microbial interactions on the biofilm ecology and pathogenesis
Yung-Hua Li et al. – AIMS Bioengineering
The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning Sixteen Years
Nicole Acosta et al. – Annals of the American Thoracic Society
Human epitelial microbiome
A tale of two risks: smoking, diabetes and the subgingival microbiome
Sukirth M. Ganesan et al. – The ISME Journal
Quantitative proteomic analysis of host epithelial cells infected by Salmonella enterica serovar Typhimurium
Linlu Qi et al. – Proteomics
Human gut microbiome
Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding
Zehra Esra Ilhan et al. – The ISME Journal
Microbe Profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa
Willem M de Vos – Microbiology
Fecal Microbiota Transplantation: From Clostridium difficile to Inflammatory Bowel Disease
Robert J. Gianotti & Alan C. Moss – Gastroenterology & Hepatology
Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome
Tao Zuo et al. – Gut
Microbial diseases
Review: ‘Omic’ Approaches to Study Uropathogenic Escherichia coli Virulence
Alvin W. Lo et al. – Trends in Microbiology
Case report: Ecthyma Gangrenosum: Escherichia coli or Pseudomonas aeruginosa?
Mohamed Abbas et al. – Frontiers in Microbiology
General environmental microbiology
Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Felix Goldschmidt et al. – The ISME Journal
Animal microbiome
Thesis: Biotic and Abiotic Factors Influence Formation and Ontogenic Dynamics of Molecularly Defined Gastro-Intestinal Microbial Communities in Lake Sturgeon (Acipenser Fulvescens) and Channel Catfish (Ictalurus Punctatus)
Abdul Razak – Michigan State University
Plant, root, and soil microbiome
Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities
Barbara Drigo et al. – Environmental Microbiology
The biogeographic pattern of microbial functional genes along an altitudinal gradient of the Tibetan pasture
Qi Qi et al. – Frontiers in Microbiology
Communication: Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey
Dong Liu et al. – Applied Soil Ecology
Letter: Leaf bacterial diversity mediates plant diversity and ecosystem function relationships
Isabelle Laforest-Lapointe et al. – Nature
Soil amendments influence Pratylenchus penetrans populations, beneficial rhizosphere microorganisms, and growth of newly planted sweet cherry
Tristan T. Watson et al. – Applied Soil Ecology
Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing
Yi Yang et al. – PLoS One
Soil Warming Increases Arsenic Availability in the Rice Rhizosphere
Rebecca B. Neumann et al. – Agricultural & Environmental Letters
Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage
Gajender Aleti et al. – Scientific Reports
Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome
Jean-Michel Hilly et al. – Plant Biotechnology Journal
A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization
Wayne Dawson et al. – Frontiers in Microbiology
Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling
Linwei Wu et al. – The ISME Journal
Book chapter: Cannabis Endophytes and Their Application in Breeding and Physiological Fitness
Parijat Kusari et al. – Cannabis sativa L. – Botany and Biotechnology
Water, estuarine and sediment microbiome
Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
Zarraz M.-P. Lee et al. – Frontiers in Microbiology
Microbes influence the biogeochemical and optical properties of maritime Antarctic snow
Hodson, AJ et al. – Journal of Geophysical Research
Bacterial diversity in Shahu lake, northwest China is significantly affected by nutrient composition rather than location
Jing-Yu Li et al. – Annals of Microbiology
Built environment
Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms
Keri Ann Lydon et al. – Elementa Science
Thesis: Characterization of Microbial Contaminants Associated with Floor Material Types
Mridula Gupta – The Ohio State University
Microbial biotechnology
Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes
Heng Zhang et al. – Frontiers in Microbiology
Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process
Hongyi Chen et al. – Annals of Microbiology
Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways
Yi-Lung Chen et al. – Cell Chemical Biology
An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield
Umesh K. Bageshwar et al. – Applied and Environmental Microbiology
Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi
Nicholas O. Igiehon & Olubukola O. Babalola – Applied Microbiology and Biotechnology
Food microbiology
Removal of foodborne pathogen biofilms by acidic electrolyzed water
Qiao Han et al. – Frontiers in Microbiology
General microbiology and evolution
Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes
Amoozegar MA et al. – Microbiology
Surface sensing for flagellar gene expression on solid media in Paenibacillus sp. NAIST15-1
Kazuo Kobayashi et al. – Applied and Environmental Microbiology
Complete genome sequence of a denitrifying bacterium, Pseudomonas sp. CC6-YY-74, isolated from Arctic Ocean sediment
Xuenzheng Lin et al. – Marine Genomics
Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species
Himel N. Khaleque et al. – Genome Announcements
Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems
Scarlett Alonso-Carmona et al. – Genome Announcements
Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida
Peili Cao et al. – Frontiers in Microbiology
Phages and viruses
Review: Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Stephen Hayes et al. – Viruses
Bioinformatics and statistics
Predicting microbial interactions from time series data with network information
Yan Wang et al. – International Journal of Data Mining and Bioinformatics
Commentary: Bioinformatics can boost metabolomics research
René Meier et al. – Journal of Biotechnology
Techniques and methods
Thesis: Carbon dioxide titration method for soil respiration measurements
Luis Martín Rubio – Tampere University of Applied Sciences
Protocol: Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities
Sujal Phadke et al. – PCR
An optimized extraction method to remove humic acids interferences from soil samples prior to microbial proteome measurements
Chen Qian & Robert L. Hettich – Journal of Proteome Research
Microbes in the news
Gene Drives Could Wipe Out Insect-Borne Disease — But What’s the Price?
Shelly Fan – Ontological Design
Non-microbiology picks
Application of mass spectrometry-based metabolomics approaches for food safety, quality and traceability
María Castro-Puyana et al. – Trends in Analytical Chemistry
Hunting for Nature’s Treasures or Learning from Nature?: The Narrative Ambivalence of the Ecotechnological Turn
Sanne van der Hout & Martin Drenthen – Berghahn Journals
What if you can workout while keeping cool with a pleasant smell ? In today’s post, read about researchers from MIT who have developed a ‘breathable workout suit’ using humidity-sensitive E.coli that can take care of cooling you down as you sweat.
Human vaginal microbiome
Early pregnancy vaginal microbiome trends and preterm birth – Stout MJ – Am J Obstet Gynecol.
Human gut microbiome
Chronic consequences on human health induced by microbial pathogens: Growth faltering among children in developing countries – Nataro JP – Vaccine
The gut-brain axis in Parkinson’s disease: Possibilities for food-based therapies – Perez-Pardo P – Eur J Pharmacol.
Animal experiments
Influence of Dietary Avocado on Gut Health in Rats – Paturi G – Plant Foods Hum Nutr.
Review:
Transcriptional networks in rodent models support a role for gut-brain communication in neurogenic hypertension: A review of the evidence – Zubcevic J – Physiol Genomics
Plant, root, and soil microbiome
Review: Let the Core Microbiota Be Functional – Lemanceau P – Trends Plant Sci.
An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield – Umesh K. Bageshwar – Appl Environ Microbiol.
High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils – Min X – Chemosphere
Built environment
Pathways in bacterial and archaeal communities dictated by ammonium stress in a high solid anaerobic digester with dewatered sludge – Li N – Bioresour Technol.
Microbes in the news
Experimental athletic shirt uses bacteria to keep you cool during workouts – eParisExtra
Gut Bacteria Changes After Some Weight-Loss Surgeries – tucson.com
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
Today’s digest has some great papers in the section-Plant, root and soil microbiome
General microbiome
Concentration and Viability of Bacterial Aerosols Associated with Weather in Asian Continental Outflow: Current Understanding – D Zhang – Aerosol Science and Engineering
Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture – H Li – bioRxiv
Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides – P Mergaert – Trends in Microbiology
Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts – N Water, Air, & Soil Pollution
Animal microbiome
Impact of dietary Moringa oleifera leaves on intestinal pathogenic load and histological structure of growing rabbits raised under heat-stress conditions – AY El-Badawi – Animal Production Science
CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice – KN Chitrala – European Journal of Immunology
Meta-analysis To Define a Core Microbiota in the Swine Gut – DB Holman – mSystems
Plant, root and soil microbiome
Let the Core Microbiota Be Functional – P Lemanceau – Trends in Plant Science
Phytobiomes – Editor-in-Chief: CA Young
Bio-mining the forest ecosystem of North East India for identification of antimicrobial metabolites from fungi through submerged fermentation – SI Devi – Bioresource Technology
Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity – SL Svensson – mBio
Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research – CE Stanley – Trends in Microbiology
Soil microbial properties as affected by short-term contrasting tillages and cropping systems in a rainfed agro-ecosystem of Northern Odisha – KN Mishra – Evolutionary Ecology
Comparison of rhizosphere properties as affected by different Bt- and non-Bt-cotton (Gossypium hirsutum L.) genotypes and fertilization – M Ahamd – Environmental Monitoring and Assessment
Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity – T Yang – New Phytologist
Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils – JD Castillo – Microbial Ecology
Lipopeptides produced by B. amyloliquefaciens NJN-6 altered the soil fungal community and non-ribosomal peptides genes harboring microbial community – J Yuan – Applied Soil Ecology
The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web – P Harkes – Oikos
Food microbiology
Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes’ milk cheese – F Cardinali – International Journal of Food Microbiology
High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions – CJ Doyle – International Journal of Food Microbiology
Built environment microbiology
Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics – J Liao – Applied Microbiology and Biotechnology
Techniques
Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium – R Kumar – mSystems
Fermentation quality, in vitro digestibility and aerobic stability of total mixed ration silages prepared with whole-plant corn (Zea mays L.) and hulless barley (Hordeum vulgare L.) straw – X Yuan – Animal Production Science
Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis – Y Zhou – International Biodeterioration & Biodegradation
An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads – JM Maritz – Microbial Ecology
More microbes
HIV Persistence Alters CXCR4 Expression Patterns In OP9-DL1-Mediated Differentiation Of In Vitro Infected Human Cord Blood CD34+ Cells – T Tsukamoto – bioRxiv
Bacterial Virus Ontology; Coordinating across Databases – C Hulo – MDPI
Microbes in news
New insights into the ancestors of all complex life – University of Bristol – News
How a Usually Harmless Bacteria Ended Up Killing 18 People in Wisconsin – S Zhang – The Atlantic
Where you can check beaches for bacteria – Daily Herald
Beware: How to avoid rare flesh-eating bacteria in Chesapeake Bay – M Basch – WTOP
Gut Microbiome Affects Two Nervous System Diseases – AL Komarrof – Journal Watch
Solution to many global challenges may be right under our feet – G Dufficy – AgriLand
Bugging cancer: gut bacteria and the big C – V Martinez – The Irish Times
Non-microbiology picks
Marginal Returns And Levels Of Research Grant Support Among Scientists Supported By The National Institutes Of Health – MS Lauer – bioRxiv
Conservation and restoration practices in humid climates – D Tejeda Sartorius – CAB Direct
A review on the “vine and wine” microbiomes, a fungus that can infect and kill mosquitos through interaction with the gut microbiota, an introduction to the viruses of coral reefs.
General microbiome
The Role of Microbiota and Immunobiotics in Granulopoiesis of Immunocompromised Hosts – Susana Salva – Frontiers in Immunology
Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations – Felix Goldschmidt – The ISME Journal
Human gut microbiome
TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota – Sozaburo Ihara – Journal of Gastroenterology
Review: Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions – Mark N Read – Frontiers in Immunology
Review: Genes, emotions and gut microbiota: The next frontier for the gastroenterologist – Arturo Panduro – World Journal of Gastroenterology
Animal experiments
Modulation of the gut microbiota impacts non-alcoholic fatty liver disease: a potential role for bile acids – Aafke WF Janssen – Journal of Lipid Research
Antimicrobial peptides extend lifespan in Drosophila – Gerrit Loch – PLOS ONE
Animal microbiome
Bacterial diversity of cosmopolitan Culex pipiens and invasive Aedes japonicus from Germany – Sina Zotzmann – Parasitology Research
Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria – Jan Hubert – Microbial Ecology
* Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality – Ge Wei – PNAS
Plant, root, and soil microbiome
Leaf bacterial diversity mediates plant diversity and ecosystem function relationships – Isabelle Laforest-Lapointe – Nature
Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – The ISME Journal
* Review: From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept – Ignacio Belda – Frontiers in Microbiology
Phages and viruses
Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations – Maria A Bautista – Viruses
* Review: Virus–host interactions and their roles in coral reef health and disease – Rebecca Vega Thurber – Nature Reviews Microbiology
Metabolomics
Inter-individual Recovery of the Microbiota and Metabolome Over Time Following Fecal Microbiota Transplantation in Patients with Recurrent Clostridium difficile Infection – Anna M Seekatz – bioRxiv
Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice – Daxesh P Patel – PLOS ONE
Review: Livestock metabolomics and the livestock metabolome: A systematic review – Seyed Ali Goldansaz – PLOS ONE
Techniques
Review: A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia – Antonella Succurro – Journal of Bacteriology
More microbes
Decoding and reprogramming fungal iterative nonribosomal peptide synthetases – Dayu Yu – Nature Communications
Microbes in the news
Companies Pursue Diagnostics that Mine the Microbiome – Andrea Anderson – The Scientist
The fungal microbiome contributes to alcohol-induced liver damage in mice – EurekAlert
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
Today’s microbiome is packed with thought-provoking insights from the status of Microbiology today and in-depth look at what is REALLY in our drinking water.
General Microbiome and Microbiology
Big Questions in Microbiology Mizrahi V. Cell
Human gut microbiome
Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Rath S. Microbiome
The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.Hibberd MC. Science Translational Medicine
Human microbiome and immune system
Potential Impact of Nutrition on Immune System Recovery from Heavy Exertion: A Metabolomics Perspective.Nieman DC. Nutrients
Animal and insect microbiome
Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. Gontang EA. Plus One
A metagenomic approach to discover a novel β-glucosidase from bovine rumens. Suwan E. Pure and Applied Chemistry, 2017
Plant, soil, and air microbiome
Tomato root microbiota and Phytophthora parasitica-associated disease. Larousse M. Microbiome
Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Oono R. Environmental Microbiology
Carbon‐driven enrichment of the crucial nitrate reducing bacteria in limed peat soil microcosms. Zhu Y. Letters in applied Microbiology
Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash. Cruz-Paredes C. Soil Biology and Biochemistry.
Inland waters and ocean microbiome
Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor.Gantt SE.FEMS Microbiology Letters.
Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pond. Lee ZMP. Frontiers in Microbiology
Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance’s perspective. Zhang Y. Environmental Microbiology
Faecal microbiome
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.Khanna S. Microbiome
Probiotics
Antioxidant Properties of Probiotic Bacteria. Wang Y. Nutrients
STUDYING HOST-MICROBIOTA MUTUALISM USING GNOTOBIOTIC DROSOPHILA. Ma D.Old Herborn University Seminar Monograph 30
Virology
Pre-Symptomatic Diagnosis of Ebola Virus Infection. Navalkar K. Emerging disease and Virology 2017
Succession in the petroleum reservoir microbiome through an oil field production lifecycle.Vigneron A. The ISME Journal
Preprint
Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. Laroche O. PeerJ
Events and jobs
Microscopist Asbestos/Microbiology – EMSL Analytical, Seattle, WA
Technician (Microbiology Team) – AsureQuality (AQ), Christchurch, Canterbury, New Zealand
Laboratory Technician I (Microbiology & Genetics) – IDEXX, Columbia, MO, US
Associate Scientist Molecular Microbiology – CheckMark Labrecruitment, South Holland
Human respiratory microbiome
Review: Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides – Wilmore C. Webley – Respiratory Research
Human gut microbiome
Review: The bidirectional gut-brain-microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease – Mark Sundman – Brain, Behavior, and Immunity
Clinical Trial Watch: ‘Targeting the gut-liver axis in liver disease’ – Reiner Wiest – Journal of Hepatology
Gluten-degrading bacteria are present in the human small intestine of healthy volunteers and celiac patients – Alexandra R. Herran – Research in Microbiology
The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans – Lloyd S. Robinson – Journal of Biological Chemistry
Plant, root, and soil microbiome
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation – José A. Siles A. Siles – Scientific Reports
Review: Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens – Ikkei Shikano – Journal of Chemical Ecology
Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots – Robert J. Dorosky – Applied and Environmental Microbiology
Water and extremophile microbiome
Review: A multiomics approach to study the microbiome response to phytoplankton blooms – Liyan Song – Applied Microbiology and Biotechnology
Antibiotics/probiotics/prebiotics
The Resistome Of Important Human Pathogens – Christian Munck – bioRxiv
Phages and viruses
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer – Marie Touchon – Current Opinion in Microbiology
Part of a themed issue on MGE-HGT in prokaryotes
Bioinformatics
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees – Märt Roosaare – PeerJ
Microbes in the news
Bacteria could lead to cleaner methane power – Jon Fingas – Engadget
Luminous bacteria will help to measure radioactivity – Siberian Federal University – EurekAlert!
A ‘Superbug’ Fungus Is Spreading Across The US – Kristen V. Brown – Gizmodo
Research shows that gut bacteria tells their hosts what to eat – Cordis News
Indian researchers use a novel route to kill TB bacteria – R. Prasad – The Hindu
Bacteria Hysteria
Cash is even grosser than you knew: Dangerous bacteria survive on paper money, study finds – James Dennin – AOL
Microbiome Digest - Bik's Picks 