Category Archives: Microbes and the market

July 3, 2017

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Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti –  Microbiome

 
Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

 
Human respiratory microbiome

 
Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

 
Human gut microbiome

 
Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang –  Toxicological Science

 
Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

 
Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

 
Animal microbiome 

 
A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans –  Molecular Ecology

 
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li –  Current Microbiology

 
Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

 
Plant, root, and soil microbiome

 
Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar –  Biotech

 

Water and extremophile microbiome

 
Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus –  bioRxiv

 
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

 
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón –  BMC Genomics

 
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

 
Food microbiology

 

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

 

Probiotics / prebiotics

 
A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

 
Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

 
Phages and viruses

 
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

 
Biotechnology

 
Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

June 30, 2017

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A few gut microbiome reviews, apparently a simple bacterial community in bullet ants, circadian rhythm of rhizosphere bacterial communities, and you might want to think twice before you step into the ocean for a swim this summer.

General microbiology

Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities – Tahir Yusufaly & James Q. Boedicker – ePub in Physical Biology, first in arXiv

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber, R Fredrik Inglis and Rolf Kümmerli – ISME Journal

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas – Rosaria Campilongo et al. – PLoS Genetics

PrePrint: Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli – Johan H. van Heerden et al. – bioRxiv

Performance of electro-spun carbon nanofiber electrodes with conductive poly(3,4-ethylenedioxythiophene) coatings in bioelectrochemical systems – Juan J.L. Guzmana & Meryem O. Pehlivaner Kara et al. – Journal of Power Sources

Press: Bacteria-coated nanofiber electrodes digest pollutants – Blaine Friedlander – Phys.org

Human skin microbiome

Review: Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin – Katharina Bitschar et al. – Journal of Dermatological Science

Human gut microbiome

Review: The nutrition-gut microbiome-physiology axis and allergic diseases – Craig McKenzie – Immunological Reviews

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease – Ashton JJ et al. – Medicine (Baltimore)

Review: The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology – Nathan T. Porter and Eric C. Martens – Annual Reviews of Microbiology

Review: Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy – Rosita Aitoro et al. – Nutrients

Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients – Qing He & Yuan Gao et al. – GigaScience

Animal experiments

PrePrint: Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes – Matthew L Jenior et al. – bioRxiv

Animal microbiome

PrePrint: Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology – Ashley L. Marcinkiewicz et al. – bioRxiv

Diversity and Persistence of the Gut Microbiome of the Giant Neotropical Bullet Ant – Corrie S. Moreau & Benjamin E. R. Rubin – Integrative and Comparative Biology

PrePrint: Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang & Daniel Rozen – bioRxiv

Plant, root and soil microbiome

Effects of habitat constraints on soil microbial community function – Naoise Nunan et al. – Scientific Reports

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism – Christopher Staley et al. – Microbiome

Biological control of Pythium, Rhizoctonia and Sclerotinia in lettuce: the plant protective activity of the bacterium Paenibacillus alvei K165 is associated with the induction of systemic resistance – G. Fatouros et al. – Plant Pathology

Water and extremophile microbiome

Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome – Gerald K. Matar & Samik Bagchi et al. – Water Research

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo et al. – Journal of Microbiological Methods

Built environment

Hospital Building and Healthcare Associated Infections (HAIs) in terms of total contamination data and cases grouped by department/areas – Shadha M. Abbas Al Asadi – Scientific Journal of Medical Research

Microbes in the news

The Bugs That Keep Us Safe – Maria-Luisa Alegre – American Journal of Transplantation

Study on human skin microbiome finds archaea abundance associated with age – Phys.org

The Dust Storm Microbiome – Weismann Institute of Science – Laboratory Equipment

Starbucks’ iced coffee may have fecal bacteria in it — so do all these other things – Donovan Harrell – Miami Herald (BBC investigation)

Bacteria change a liquid’s properties and escape entrapment – Gail Mccormick – Phys.org

Only association: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows – DailyMail

Elevated bacteria counts found at 4 Island beaches – Rick Kelley – Valley Morning Star

Plasmids: traffickers of antibiotic resistance – Modernising Medical Microbiology – University of Oxford

Microbes on the market

Diabetes: J&J and Seventure Partners launch investment – tg – European Biotechnology

Global Microbiome Drugs Market 2017- Pfizer, Second Genome , Seres Therapeutics, MaaT Pharma, Enterome Bioscience – Nakul Shirke – Daily Hover

June 25, 2017

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Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

June 22, 2017

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Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 21, 201

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Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.

Events and jobs

Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain

Quality Associate Specialist – Merck, Durham, NC, US

Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome

A null model for microbial diversification – Timothy J. Straub – PNAS

Pregnancy and early life

Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome

Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome 

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal

Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome 

Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal

Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal

Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal

Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori –  Nature Communications

Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz –  PNAS

Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? – Anne D. Jungblut – Proceedings of the Royal Society B

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses

Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –

Microbes in the news 

Zombie bacteria and viruses in melting permafrost are waking up  

ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research

Gut microbiome changes linked to numerous biomarkers of type 2 diabetes 

Funky tasting beer? Biofilms may be to blame, MSU researchers say

Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes

Microbes on the market

This Company Uses the Human Microbiome to Discover New Disease Mechanisms

June 14, 2017

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Still quite a few articles on rhizosphere, and antibiotic resistance remains a hot topic, both in the literature and media. How about a Micro-lympics?

Jobs

Microbiology Technician – Seattle Washington

Events

*Annual Microbiology Retreat µlympics – Indiana University

General microbiology

*Commentary: History of Medicine: Origin of the Term Microbiome and why it Matters – Susan L. Prescott – Human Microbiome Journal

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project – Briana Vecchio-Pagan – Frontiers in Microbiology

Adaptor protein mediates dynamic pump assembly for bacterial metal efflux – Ace George Santiago et al. – PNAS

Press: E. coli bacteria’s defense secret revealed – Bill Steele – Phys.org

Uncharacterized bacterial structures revealed by electron cryotomography – Megan J. Dobro et al. – Journal of Bacteriology

Press: Researchers discover new structures in bacteria, seek to determine function – Phys.org

Microbots decorated with silver nanoparticles kill bacteria in aqueous media – Diana Vilela et al. – Applied Materials and Interfaces

Human gut microbiome

Book chapter: The gut microbiome and inflammatory bowel disease – Maire A. Conrad et al. – Pediatric Inflammatory Bowel Disease (Ed. Petar Mamula et al.)

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis – Ines Thiele et al. – Current Opinion in Systems Biology

Human nearly-sterile sites

Endometrial microbiota—new player in town – Inmaculada Moreno & Jason M. Franasiak – Fertility and Sterility

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F. Gomez-Arango et al. – Scientific Reports

Plant, root and soil microbiome

Stability and dynamics of enzyme activity patterns in the rice rhizosphere: Effects of plant growth and temperature – Tida Ge et al. – Soil Biology and Biochemistry

Doctoral thesis: Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes – Hua Xiao – Virginia Tech

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac – Jinping Wu et al. – World Journal of Microbiology and Biotechnology

*Fishing bacteria with a nanonet – F. De Cesare et al. – Materials Today

Isolation, identification, characterization, and screening of rhizospheric bacteria for herbicidal activity – Charles Oluwaseun Adetunji et al. – Organic Agriculture

Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US – Chuntao Yin et al. – Phytobiomes

*Dispersal enhances beta diversity in nectar microbes – Rachel L. Vannette & Tadashi Fukami – Ecology Letters

Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes – Florine Degrune et al. – Frontiers in Microbiology

Water and extremophile microbiome

Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste – German A. Estrada-Bonilla et al. – Systematic and Applied Microbiology

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor – Noah Stern et al. – Applied and Environmental Microbiology

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – I.L. Angell et al. – Letters in Applied Microbiology

Built environment

The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries – Anders B Nygaard & Colin Charnock – Indoor and Built Environment

Factors Determining the Biodiversity of Halophilic Microorganisms on Historic Masonry Buildings – Anna Otlewska et al. – Microbes and Environments

Phages and viruses

The pepper virome: natural co-infection of diverse viruses and their quasispecies – Yeonhwa Jo et al. – BMC Genomics

Bioinformatics

A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni et al. – Journal of Microbiological Methods

*PrePrint: Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software – Alexander Sczyrba et al. – bioRxiv

Microbes in the news

Live antibiotics use bacteria to kill bacteria – Elizabeth Eaton – Science News

Will a New Drug to Fight Antibiotic Resistant Bacteria Really Work? – Shawn Radcliffe – Healthline news

Former Pfizer Scientist Is Resurrecting Projects To Solve The Multidrug Resistant Bacteria Problem – John LaMattina – Forbes

The Algae That Devastated Florida’s Coasts Also Contained 28 Kinds Of Bacteria, Study Finds – Kate Stein – WGCU

Microbes on the market

DoggyBiome: studying the microbiome to improve dog health – AnimalBiome – Backerkit

Science, career and publishing

Book chapter: Women of Science – Laura E. Willis – Viewpoints on Media Effects: Pseudo-reality and Its Influence on Media Consumers (Ed. Carol M. Madere)

PrePrint: An elective course for medical students on innovation and entrepreneurship – Erik Reinertsen et al. – bioRxiv

June 9, 2017

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Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today

May 17, 2017

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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!

May 13, 2017

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Events and jobs

Microbiology/Molecular Biology/Wildlife Disease Technician: Wisconsin – USGS – National Wildlife Health Center

Sr. Associate, Quality Control Microbiology – Moderna

Staff Research Associate, Anaerobic Microbiology – UC Berkeley

General microbiome

Perspective: The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals – Alfredo Franco-Obregón – mSystems

Human gut microbiome

Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts – Elizabeth R Volkmann – BMJ Open Gastroenterology

Review: Microbiota: Clostridia protect from gut infections in early life – Irene Vacca – Nature Reviews Microbiology

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

Plant, root, and soil microbiome

Bacterial root microbiome of plants growing in oil sands reclamation covers – Eduardo Kovalski Mitter – Frontiers in Microbiology

Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot – Kandasamy Saravanakumar – Scientific Reports

Water and extremophile microbiome

Characterisation of Arctic Bacterial Communities in the Air above Svalbard – Lewis Cuthbertson – Biology

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island – Garabed Antranikian – Extremophiles

Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake – Mylène Hugoni – Aquatic Microbial Ecology

Distribution and activity of benthic bacteria in four lakes in the Bory Tucholskie National Park (Poland) – Łukasz Kubera – Aquatic Microbial Ecology

Role of EPS, Dispersant and Nutrients on the Microbial Response and MOS Formation in the Subarctic Northeast Atlantic – Laura Duran Suja – Frontiers in Microbiology

Food microbiology

Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor – Igor Magalhães da Veiga Moreir – Molecules

Techniques

Harnessing the power of digital droplet PCR to conduct real-world microbial competitions – Helen A. Murphy – Molecular Ecology Resources

Microbes in the news

Lung microbiome – Sally Robertson – News-Medical.Net

Resistant Starch from Potatoes Offers Benefits to Gut Microbiome? – Michael Crane – Nutritional Outlook

Visualizing the Microbiome through Handmade Embroidery – Clara Rodríguez Fernández – labiotech

Microbes on the market

‘Imagine being able to edit the microbiome’ – TechAccel talks animal nutrition targeted innovation – Aerin Einstein-Curtis – Feed Navigator

Science, publishing, and career

Weill Cornell Aims For ‘Precision Metagenomics’ With Quantitative Computing – Neil Versel – GenomeWeb

May 10, 2017

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A short digest today, but not without interesting pieces. Largest study yet to demonstrate vertical transfer of bacteria from mother to infant, microbes could orchestrate plant ‘migration’, and many fascinating pieces of news on microbes. How may we make peace with microbes in and around us?

General microbiology

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance – Asunción Delgado et al. – Cell Reports

Press: Four-billion-year-old ‘fossil’ protein resurrected in bacteria protects them from viruses – Phys.org

Infant Gut Microbiome

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj et al. – JAMA Pediatrics

Press: Breastfeeding plays important role in ‘seeding’ infant microbiome with beneficial bacteria – Leigh Hopper – UCLA

Plant, root and soil microbiome

Microbial communities and diazotrophic activity differ in the root-zone of Alamo and Dacotah switchgrass feedstocks – Richard R. Rodrigues et al. – Global Change Biology Bioenergy

Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics – Michael E. Van Nuland et al. – Nature Ecology and Evolution

Press: Microscopic soil creatures could orchestrate massive tree ‘migrations’ – University of Tennessee at Knoxville – Science Daily

Microbes in the news

Global warming is altering the microbiota of lizards – Brooks Hays – UPI

TOO much exercise causes a leaky gut and increases health risks, research shows (and be especially careful if you work in the military) – Claudia Tanner – Daily Mail

Be wary of the title: Bacteria in Yogurt Cures Depression, Study Shows – Lorie Johnson – CBN News

Anecdotal evidence: Faecal transplants boost mind-gut link – Sarah Wiedersehn – Yahoo News

Bacteria appears to be behind mysterious outbreak in Liberia – Mike Stobbe – ABC News

Scientists Battle Bacteria with Silver and Mucus – Shawn Radcliffe – Healthline News

Verify: Will I contract flesh-eating bacteria at the beach in Texas? – Brandon Jones – KVUE

BACTERIA could mean the end of the pothole: Radical self repairing road can ‘grow’ into cracks – Cecile Borkhataria – Daily Mail

I Survived Flesh-Eating Bacteria—and It Changed My Life Forever – Aimee Copeland – Time

Microbes on the market

Oral enzyme prevents C. difficile infection, VRE colonization – Healio Gastroenterology