Category Archives: Food Microbiology

March 1, 2017

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Today’s digest features interesting reviews on the tole of gut microbiota in chronic kidney disease, and biotoxicity of soils from Mars. Impact of altered gut microbiota on bone strength in mice. Enjoy!

Events and jobs

Technical Service Representative (Microbiology) – ThermoFisher Scientific – Lenexa, Kansas

General microbiome

Review: Microbe social skill: the cell-to-cell communication between microorganisms – Xi Zhao – Science Bulletin

Review: Creating new business, economic growth and regional prosperity through microbiome-based products in the agriculture industry – Brajesh K. Singh – Microbial Biotechnology

Review: The link between inflammation, bugs, the intestine and the brain in alcohol dependence – S Leclercq – Translational Psychiatry

Editorial: The human microbiome: an emerging tool in forensics – Jarrad T. Hampton-Marcell – Microbial Biotechnology

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome – Ohad Manor – Cell Host and Microbe

Pregnancy and early life

Review: Transfer of maternal psychosocial stress to the fetus – Florian Rakers – Neuroscience & Biobehavioral Reviews

Vaginal microbiome

Survival of vaginal microorganisms in three commercially available transport systems – Allison L. DeMarco – Anaerobe

Human skin microbiome

Review: Towards personalized modification of microbial imbalances – J.E.E. Totté – British Journal of Dermatology

Human gut microbiome

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

*Review: Gut microbiota in chronic kidney disease – Secundino Cigarran Guldris – Nefrología (English Edition)

Review: The clinical value of breath hydrogen testing – Chu K Yao – Journal of Gastroenterology and Hepatology

Commentary: Atopic dermatitis and gut microbiota – M. Lindberg – British Journal of Dermatology

Animal experiments

SYN-004 (ribaxamase), an Oral Beta-Lactamase, Mitigates Antibiotic-Mediated Dysbiosis in a Porcine Gut Microbiome Model – Sheila Connelly – Journal of Applied Microbiology

*Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Plant, root, and soil microbiome

*Biotoxicity of Mars Soils: 2. Survival of Bacillus subtilis and Enterococcus faecalis in Aqueous Extracts Derived from Six Mars Analog Soils – Andrew C. Schuerger – Icarus

Food microbiology

Polyphenolic extracts of cherry (Prunus cerasus L.) and blackcurrant (Ribes nigrum L.) leaves as natural preservatives in meat products – Agnieszka Nowak – Food Microbiology

Probiotics / prebiotics

Effects of synbiotic supplementation on growth performance, carcass characteristics, meat quality and muscular antioxidant capacity and mineral contents in broilers – Yefei Cheng – Journal of the Science of Food and Agriculture

GH11 xylanase increases prebiotic oligosaccharides from wheat bran favouring butyrate-producing bacteria in vitro – Jonas Laukkonen Ravn – Animal Feed Science and Technology

Effects of Bacillus subtilis strains and the prebiotic Previda® on growth, immune parameters and susceptibility to Aeromonas hydrophila infection in Nile tilapia, Oreochromis niloticus – Samuel Addo – Aquaculture Research

Enhancing growth and resistance to Vibrio alginolyticus disease in catarina scallop (Argopecten ventricosus) with Bacillus and Lactobacillus probiotic strains during early development – Fernando Abasolo-Pacheco – Aquaculture Research

The association of a probiotic with a prebiotic (Flortec, Bracco) to improve the quality/quantity of spermatozoa in infertile patients with idiopathic oligoasthenoteratospermia: a pilot study – C. Maretti – Andrology

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – Dong Ji-lin – Journal of the Science of Food and Agriculture

Microbes in the news 

WHO: These 12 bacteria pose greatest risk to human health

A Bizarre Bacteria Could Be the Key to Controlling Mosquitoes

Flesh-eating bugs lurking on ATMs and killer bacteria found on phones

Microbes on the market 

Proof-of-Concept Study Published in Clinical Microbiology and Infection Reports the Benefit of PathoQuest NGS-Based Metagenomics Test to Identify Clinically-Relevant Pathogens in Immunocompromised Patients Suspected of Infection

Anitha’s non-microbiology picks

Glass Microbiology at the At-Bristol Science Centre

Mysterious ‘Cosmic’ Jellyfish Spotted in Remote Ocean Depths

Unity Biotechnology: Investment In A Long And Healthy Life Becoming Possible

February 27, 2017

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The ‘horseshoe effect’ in analyzing microbial niches; fecal microbiota transplantation (FMT) in immunocompromised individuals; effects of long-term ceftriaxone sodium administration on gut microbiota diversity; DNA extraction bias in soil microbial community analysis; and a multistrain probiotic clinical trial in NAFLD.

Events and jobs

Postdoctoral Fellow in Microbiology – University of Tennessee Health Science Center, Memphis, TN

QC Microbiology Analyst – Leidos – Frederick, MD

General microbiome
Uncovering the Horseshoe Effect in Microbial Analyses – James T. Morton – mSystems

Pregnancy and early life
Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Implications of intrapartum azithromycin on neonatal microbiota – Jenny Mei – The Lancet Infectious Diseases

Human respiratory microbiome
Restoring CFTR Function Reduces Airway Bacteria and Inflammation in People With Cystic Fibrosis and Chronic Lung Infections – Katherine B. Hisert – American Journal of Respiratory and Critical Care Medicine

Microbiome of the Lung in Patient with Idiopathic Pneumonia Syndrome (IPS) after HCT – Sachiko Seo – Biology of Blood and Marrow Transplantation

Oral and nasal microbiota in Parkinson’s disease – Pedro A.B. Pereira – Parkinsonism & Related Disorders

Human skin microbiome
N-acetylcysteine inhibits growth, adhesion and biofilm formation of Gram-positive skin pathogens – Daria Eroshenko – Microbial Pathogenesis

Human vaginal microbiome
Olegusella massiliensis gen. nov., sp. nov., strain KHD7T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis – Khoudia Diop – Anaerobe

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobe

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women – Vodstrcil LA – PLoS One

Human gut microbiome
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system – Yanjie Guo – Scientific Reports

Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota – Danielle N. Cooper – Nutrients

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Gut microbiota and systemic inflammation changes after bread consumption: The ingredients and the processing influence – Maykel Arias – Journal of Functional Foods

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wong – Microbial Pathogenesis

The dual role of short fatty acid chains in the pathogenesis of autoimmune disease models – Mizuno M – PLoS One

Giardia duodenalis induces dysbiosis of human intestinal microbiota biofilms – Jennifer K. Beatty – International Journal for Parasitology

Animal experiments
Apple Polysaccharide inhibits microbial dysbiosis and chronic inflammation and modulates gut permeability in HFD-fed rats – Sheng Wang – International Journal of Biological Macromolecules

Animal microbiome
Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle – Fuyong Li – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Review: Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding – Samuel Kroll – Current Opinion in Plant Biology

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬ – Ines Aline Aschenbrenner – Molecular Ecology

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils – Adrienne B. Narrowe – Environmental Microbiology

A comprehensive phylogenetic analysis of copper transporting P1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes – Ciro Cubillas – Microbiology Open

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Loss of soil microbial diversity may increase insecticide uptake by crop – Min Zhang – Agriculture, Ecosystems & Environment

The presence of aggressive ants is associated with insect visits to coffee flowers and floral microbe communities – Rachel L. Vannette – Basic and Applied Ecology

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy – P. Bhattacharyya – Science of the Total Environment

The Introduction of Woody Plants For Freshwater Wetland Restoration Alters The Archaeal Community Structure in Soil – Xiao-Yan Liu – Land Degradation & Development

A distinctive root-inhabiting denitrifying community with high N2O/(N2O+N2) product ratio – Chao Ai – Soil Biology and Biochemistry

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Water and extremophile microbiome
Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds – Jingjing Wang – International Aquatic Research

Serpentinization-influenced groundwater harbors extremely low diversity microbial communities adapted to high pH – Katrina I. Twing – Frontiers in Microbiology

Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi – Timothy J. Williams – Environmental Microbiology

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of the Total Environment

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters – Carmen Falagán – Extremophiles

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms – Timothy Sibanda – Microbial Biotechnology

Acinetobacter halotolerans sp. nov., a novel halotolerant, alkalitolerant, and hydrocarbon degrading bacterium, isolated from soil – Ram Hari Dahal – Arhives of Microbiology

Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature – Robert Ccorahua-Santo – Research in Microbiology

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – Microbiology Open

Food microbiology
Nondairy beverage produced by controlled fermentation with potential probiotic starter cultures of lactic acid bacteria and yeast – Ana Luiza Freire – International Journal of Food Microbiology

Probiotics / prebiotics
Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice – Aurelijus Burokas – Biological Psychiatry

Review: Clinical effects of probiotics in cystic fibrosis patients: A systematic review – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Effects of Multistrain Probiotic Supplementation on Glycemic and Inflammatory Indices in Patients with Nonalcoholic Fatty Liver Disease: A Double-Blind Randomized Clinical Trial – Abbaszadeh Sepideh – Journal of the American College of Nutrition

Microbes in the news
Glass Microbiology at the At-Bristol Science Centre – Culture Calling

Bacteria And Babies: A Scientific Debate – Part One – American Council on Science and Health

Reference: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns – Maria G. Dominguez-Bello – PNAS

February 23, 2017

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Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 16, 2017

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Events and jobs

 Microbiology assistant or associate professor – Universidad de los Andes (Bogotá, Colombia)

PhD – Mechanisms of bacterial community dynamics in oral biofilms – The University of Sheffield, UK

General microbiome

Microbiome and Cardiac Health – Enrico Biffi – Integrative Cardiology

Editorial: Signals to sociality: how microbial communication fashions communities – Karine A. Gibbs – FEMS Microbiology Reviews

Pregnancy and early life

Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial – Wafaa Qasem – BMC Pediatrics

Human oral microbiome

Dysbiosis of oral buccal mucosa microbiota in patients with oral lichen planus – Yuan He – Oral Diseases

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis – Dongmei Ai – BMC Genomics 2017

Human respiratory microbiome

Bacterial Topography of the Healthy Human Lower Respiratory Tract – Robert P. Dickson – American Society for Microbiology (mBio)

Human vaginal microbiome

Distinct effects of the cervico-vaginal microbiota and herpes simplex type 2 infection on female genital tract immunology – Shannon B. – The Journal of Infectious Diseases

Human gut microbiome

DIFFERENCES IN GUT MICROBIOTA ACTIVITY (ANTIMICROBIALS, POTENTIAL MUTAGENS, AND STEROLS) ACCORDING TO DIET – P. OLEJNÍKOVÁ – Acta Alimentaria

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leeuwenhoek

Diversity and enterotype in gut bacterial community of adults in Taiwan – Chao Liang – BMC Genomics

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn’s disease in the Ryukyu Islands – Shigeki Nakagome – Human Genetics

Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention – Guojun Wu – American Socieity for Microbiology (mBio)

Review: Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases – Lieke WJ van den Elsen – Clinical and Translational Immunology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes – Julia H. Kreznar – Cell Reports

Melatonin prevents obesity through modulation of gut microbiota in mice – Pengfei Xu – Journal of Pineal Research

Inonotus obliquus polysaccharide regulates gut microbiota of chronic pancreatitis in mice – Yang Hu – AMB Express

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet – Sophie Comtet-Marre – Frontiers in Microbiology

Animal microbiome

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island – Jan M. Meyer – Environmental Microbiology

Plant, root, and soil microbiome

Effect of Elevated UV-B Radiation on Microbial Biomass C and Soil Respiration in Different Barley Cultivars Under Field Conditions – Yunsheng Lou – Water, Air, Soil Pollution

Comment: Isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of Maize seedlings in greenhouses – Jeffrey S. Norman – Frontiers in Plant Science

Effects of Vegetation and Temperature on Nutrient Removal and Microbiology in Horizontal Subsurface Flow Constructed Wetlands for Treatment of Domestic Sewage – Qingwei Zhou – Water, Air, Soil Pollution

Editorial: Biotrophic Plant-Microbe Interactions – Pietro D. Spanu – Frontiers in Plant Science

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA – Kathleen H. Lavoie – PloS ONE

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community – Lu Shi – Scientific Reports

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank – Marcio F. A. Leite – Scientific Reports

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil – Pengfei Liu – Environmental Microbiology

Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles – C. F. McGee – Ecotoxicology

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system – Jun Zhao – Environmental biotechnology

Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil – Manli Wu – Environmental Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems – Celine Pisapia – Frontiers in Microbiology

Food microbiology

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases – David F. Nieuwenhuijse – Frontiers in Microbiology

Masters Thesis: Effects of Cavitation on the Removal and Inactivation of Listeria and Salmonella from the Surface of Tomatoes and Cantaloupe – Joshua Jungho Lee – Virginia Tech

Chemical characterization of the glycated myofibrillar proteins from grass carp (Ctenopharyngodon idella) and their impacts on the human gut microbiota in vitro fermentation – Kaining Han – Food & Function

Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination – Etienne V. Doll – Frontiers in Microbiology

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products – Aoife J. McHugh – Frontiers in Microbiology

Probiotics / prebiotics

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota – V.D.V. Valeriano – Journal of Applied Microbiology

Physiological Changes of Surface Membrane in Lactobacillus with Prebiotics – Mingfang Pan – Journal of Food Science

Bioinformatics

Comparative Analysis of Soil Microbiome Diversity using QIIME and CloVR Pipelines – Puniethaa Prabhu – Biometrics and Bioinformatics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman (Duke University) – eLife

MetaTopics: an integration tool to analyze microbial community profile by topic model – Jifang Yan – BMC Genomics 2017

Enhancing the clinical coverage and anticancer efficacy of immune checkpoint blockade through manipulation of the gut microbiota – Jonathon M. Pitt – OncoImmunology

Techniques         

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research – Sebastian Menke – Frontiers in Microbiology

Microbes on the market 

Day Two link with Johnson & Johnson on personalized microbiome analysis for diabetes nutrition – Eliot Beer – nutraingredients.com

Microbes in the news

News Feature: Cleaning up the hygiene hypothesis – Megan Scudellari – PNAS

Ed’s non-microbiology picks

Decline in global oceanic oxygen content during the past five decades – Sunke Schmidtko – Nature

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum – Christian Kehlmaier – Proceedings of the Royal Society (Biological Sciences)

Long-term trends in the honeybee ‘whooping signal’ revealed by automated detection – Michael Ramsey – PloS One

January 26, 2017

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Environmental ecology review presents how microbial life strategy concepts are applied in complex microbial communities.   Two interesting model systems are described in the techniques section, plus potentially scalable workflow for the preparation of high potency Akkermansia muciniphila cells for therapeutic interventions.  The importance of understanding the role of the microbiome in preventing complications after organ transplant and surgeries are discussed in two reviews.   Another study shows that proton pump inhibitors used to prevent gastric ulcers were associated with distinct gut microbiota signatures.  For faster wound healing, try some saliva. A study shows the beneficial effects of saliva on wound healing in human epidermal keratinocytes and on the attenuation of intracellular Staph. aureus infection.

Pregnancy and early life

Assessment of the synbiotic properties of human milk oligosaccharides and Bifidobacterium longum subsp. infantis in vitro and in humanised mice – S Musilova- Beneficial Microbes

Multi-site human microbiome

Review: Infection in Organ Transplantation – Jay A. Fishman – American Journal of Transplantation

Review: The gut microbiome and the mechanism of surgical infection – J.C. Alverdy – The British Journal of Surgery

Human Oral Microbiome

Salivary mucins promote the coexistence of competing oral bacterial species – Erica Shapiro Frenke- The ISME Journal

Human skin microbiome

Saliva induces expression of antimicrobial peptides and promotes intracellular killing of bacteria in keratinocytes by epidermal growth factor receptor transactivation – T. Mohanty – British Journal of Dermatology

Human gut microbiome

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota – Floris Imhann – Gut Microbes

Animal experiments

Review: Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation – Nilusha Malmuthuge  – Journal of Animal Science and Technology

Plant, root, and soil microbiome

Review: Revisiting life strategy concepts in environmental microbial ecology – Adrian Ho- FEMS Microbiology Ecology

Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice – Si Chen – Journal of Environmental Sciences

Food microbiology

Review: Human pathogens in plant biofilms: Formation, physiology, and detection – Eduardo Ximenes – Biotechnology and Bioengineering

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork -Koji Yahara – Environmental Microbiology

Digestive fate of dietary carrageenan: Evidence of interference with digestive proteolysis and disruption of gut epithelial function – Lulu Fahoum – Molecular Nutrition Food Research

Bioinformatics

It’s a big data problem: researchers from the University of California, San Diego and the J.C. Venter Institute used machine learning to teach a computer to learn to distinguish between healthy and unhealthy gut microbiomes. The new approach shows promise for predicting related health issues and providing guidance for therapy development. More from the press

Techniques

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions – JP Ouwerkerk  -Beneficial Microbes

Evaluation of colonization resistance in stool of human donors using ex vivo, in vitro and in vivo assays – MF Galvão  – Beneficial Microbes

Improving metabolite production in microbial co-cultures using a spatially constrained hydrogel – Matthew J. Smith – Biotechnology and Bioengineering

Microbes in the news

CRISPR research institute expands into agriculture, microbiology

Dog obesity, a growing problem, may be managed through diet and exercise and- microbiology

Every surfer knows you should stay out of the water for 72 hours after it rains. Public health officials issued an advisory for all Los Angeles County beaches, cautioning swimmers and surfers to stay away from areas near storm drains, creeks and rivers. But when the waves show – some surfers just can’t help themselves.

January 18, 2017

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Biogeographical patterns and assembly processes of bacterial on glaciers. And, a critical review of interactions between central nervous system and microbiota during health and neurological disease.

● Hospital microbiome

Microbiota-targeted therapies on the intensive care unit. Haak, BW . Current opinions in Critical Care

● Human microbiome and nervous system

Review: Interactions between the microbiota, immune and nervous systems in health and disease. Thomas C Fung.Nature Neuroscience

● Human gut microbiome

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Patrascu O. Scientific Report

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. Moelling, K. Bacteriophage

● Animal experiments 

Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats. Requena T. Food & Function

Effect of early antibiotic administration on cecal bacterial communities and their metabolic profiles in pigs fed diets with different protein levels. Zhang C. Anaerobe

● Animal microbiome 

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau. Wei YQ. Anaerobe

Gut microbiota isolated from the European pond turtle (Emys orbicularis) and its antimicrobial resistance. Ruzauskas M. Polish Journal of Veterinary Sciences

● Plant, root, and soil microbiome

Restoration using Azolla imbricata increases nitrogen functional bacterial groups and genes in soil. Xiao-Ming Lu. Applied Microbiology and Biotechnology

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia. Waseem M. Mycorrhiza

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.Ambrosini, R.Microbial Ecology

● Water and extremophile microbiome 

Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate. Remmas, N. Environmental Science and Pollution Research

January 17, 2017

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Bacterial content of human milk, contribution of the microbiota to serotonin and bile acid production, review of genome-scale metabolic network models, model multi-species biofilm to study formation and interaction dynamics in bioelectrochemical systems.

Pregnancy and early life

Review: Interactions between early life stress and metabolic stress in programming of mental and metabolic health – Francesca Cirulli – Current Opinion in Behavioral Sciences

A retrospective audit of bacterial culture results of donated human milk in Perth, Western Australia – Yahya Almutawif – Early Human Development

Animal experiments

Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility – Xiaolong Ge – Journal of Translational Medicine

Food microbiology

* Resilience, dynamics and interactions within a multi-species exoelectrogenic model biofilm community – Anna Prokhorova – Applied and Environmental Microbiology

Metabolomics

Review: Metabolic network modeling with model organisms – L Safak Yilmaz – Current Opinion in Chemical Biology

More microbes

Research Highlight: Evolutionary insights from the Vikings – Ashley York – Nature Reviews Microbiology

Microbes in the news

New Study Raises Specter of More Bacteria Resistant to Last Line Antibiotics – Ellie Kincaid – The Wall Street Journal

Teaching computers to recognize sick guts—machine learning and the microbiome – provided by University of California, San Diego – Phys.org

Woman Dies From Bacteria Resistant To All Antibiotics: Why Don’t More People Care? – Bruce Y. Lee – Forbes Pharma & Healthcare

Essential Science: Using bacteria to generate useful chemicals – Tim Sandle – Digital Journal

Bugs in space! Using microgravity to understand how bacteria can cause disease – Ellen Higginson – OUPblog

Are probiotics the answer for lactose intolerance? – Matt Englund – Medical Xpress

Heat & drug tolerant bacteria in Hyderabad meat triggers alarm – Syed Akbarl – The Times of India

Probiotics and Alzheimer’s: Personalised nutrition tipped to become crucial area of treatment research – Gary Scattergood – Nutraingredients.com

Microbes on the market

Global Human Microbiome Market Size, Share, Development and Demand, Forecast to 2022 – P&S Market Research – openPR

Seres Therapeutics, Inc. (MCRB) Downgraded by Zacks Investment Research – Daniel Jordon – Sports Perspectives and Market News

January 16, 2017

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Environmental pollutants have become an increasingly common health hazard. The possible effects of environmental pollutants on gut microbiota and their subsequent effects on health is discussed in highlighted review.

Pregnancy and early life

Antibiotics in Pregnancy Increase Children’s Risk of Otitis Media and Ventilation Tubes – Tine Marie Pedersen – The journal of Pediatrics

Human skin microbiome

Insights into the mast cell–microbiome connection in the skin – Alon Y. Hershko – Journal of Allergy and Clinical Immunology

Microbiota fingerprints lose individually identifying features over time – David Wilkins – Microbiome

Human vaginal microbiome

Association between preterm labor and genitourinary tract infections caused by Trichomonas vaginalis, Mycoplasma hominis, Gram-negative bacilli, and coryneforms – Alaa El-Dien M.S. Hosny – Journal of the Chinese Medical Association

The Vaginal Microbiota and Urinary Tract Infection – Ann E. Stapleton – Microbiol Spectrum

Human nearly-sterile sites 

Metabolic profiles of exudates from chronic leg ulcerations – Adam Junka – Journal of Pharmaceutical and Biomedical Analysis

Human oral microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier – Nicolas Dutzan – Immunity

Salivary Gluten Degradation and Oral Microbial Profiles in Health and Celiac Disease – Na Tian  – Applied and Environmental Microbiology

Human gut microbiome

Expert review: Management of Clostridium difficile Infection in Inflammatory Bowel Disease: Expert Review from the Clinical Practice Updates Committee of the AGA Institute – Sahil Khanna – Clinical Gastroenterology and Hepatology

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Review: The role of the gut microbiota in sepsis – Bastiaan W Haak – The Lancet Gastroenterology & Hepatology

Gut microbiota interactions with the immunomodulatory role of vitamin D in normal individuals – Renata V. Luthold – Metabolism

“Angelakisella massiliensis” gen. nov., sp. nov., a new bacterial species isolated from human ileum – Morgane Mailhe – New Microbes and New Infections

Helicobacter pylori–related metabolic syndrome as predictor of progression to esophageal carcinoma in a subpopulation-based Barrett’s esophagus cohort – Jannis Kountouras – Gastrointestinal Endoscopy

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Absence of intestinal microbiota increases ß-cyclodextrin stimulated reverse cholesterol transport – Rima H. Mistry – Molecular Nutrition & Food Research

European consensus conference on faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut
Animal experiments

Gd-DTPA-induced dynamic metabonomic changes in rat biofluids – Chuanling Wan – Magnetic Resonance Imaging

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats – Melissa N. Conley – Molecular Nutrition & Food Research

Animal microbiome

Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish – Thanh Luan Nguyen – Aquaculture

Plant, root, and soil microbiome

The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils – Agnieszka Józefowska – Geoderma

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil – Jichen Wang – Applied Soil Ecology

Water and extremophile microbiome

Effects of the halophilic fungi Cladosporium sphaerospermum, Wallemia sebi, Aureobasidium pullulans and Aspergillus nidulans on halite formed on sandstone surface – Maisa M.A. Mansour – International Biodeterioration & Biodegradation

Epiphytic Planctomycetes communities associated with three main groups of macroalgae – Joana Bondoso – FEMS Microbiology Ecology

Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments -C.J. Charles – Applied and Environmental Microbiology

Capturing compositional variation in denitrifying communities: A multiple primer approach that includes autotrophic denitrifying Epsilonproteobacteria – S.A. Murdock  – Applied and Environmental Microbiology

Waste and pollution microbiology

Review: Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation – Sevcan Aydin – Fungal Biology Reviews

Built environment 

Biological invasion in the indoor environment: the spread of Eurotium halophilicum on library materials – Andrea Polo – International Biodeterioration & Biodegradation

Review: Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins – An update – Francis Fleurat-Lessard – Journal of Stored Products Research

Food microbiology

Impact of environmental conditions and process modifications on microbial diversity, fermentation efficiency and chemical profile during the fermentation of mezcal in Oaxaca – Manuel R. Kirchmayr – LWT – Food Science and Technology

Anti-aging and redox state regulation effects of A-type proanthocyanidins-rich cranberry concentrate and its comparison with grape seed extract in mice – Jingjing Jiao – Journal of Functional Foods

Probiotics / prebiotics

Probiotic mixture improves fatty liver disease by virtue of its action on lipid profiles, leptin, and inflammatory biomarkers – Hessah Mohammed Al-muzafar – BMC Complementary and Alternative Medicine

January 14, 2017

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So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

January 13, 2017

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Nutrient acquisition by gut microbes, handling stress and gut microbiota changes in mice, evaluation of the MinION for microbiome studies.

Human gut microbiome

* Structural basis for nutrient acquisition by dominant members of the human gut microbiota – Amy J. Glenwright – Nature

New light shed on functioning of human gut bacteria – Science Daily

Metabolic adaptation of colonic microbiota to galactooligosaccharides: a proof-of-concept-study – M. Mego – Alimentary Pharmacology and Therapeutics

Gut microbiota-dependent trimethylamine N-oxide in acute coronary syndromes: a prognostic marker for incident cardiovascular events beyond traditional risk factors – Xinmin S. Li, Slayman Obeid – European Heart Journal

Review: Basic Definitions and Concepts: Organization of the Gut Microbiome – Eamonn M.M. Quigley – Gastroenterology Clinics of North America

Animal experiments

* Handling stress may confound murine gut microbiota studies – Cary R. Allen-Blevins – PeerJ

Water microbiome

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies – Laurence J. Clarke – Ecology and Evolution

Food microbiology

Cultivable microbiome of fresh white button mushrooms – W. Rossouw Letters in Applied Microbiology

Phages and viruses

Acquisition of Phage Sensitivity by Bacteria through Exchange of Phage Receptors – Elhanan Tzipilevich – Cell

For viral predators of bacteria, sensitivity can be contagious. New modes of bacteriophage spread discovered – ScienceDaily

Techniques

Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization – Xiao Ma – bioRxiv

Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria – Michał Horka – Analytical Chemistry

Press: New type of monitoring provides information about the life of bacteria in microdroplets – Science Daily

Microbes in the news

Self-Experimenting Scientist Receives uBiome Grant to Investigate Consequences of Long-Term Antibiotic Use for Skin Conditions – PR Web

The art within Microbiology, and a coloring book – Chloe Schmidt – Frontiers Blog

Mapping the Microorganisms Behind Hospital-Borne Infections – Allison Bond – The Atlantic

Springfield Science Museum Explores the Human Microbiome – Business West

Researchers receive Moore Foundation grant to study the global ocean microbiome – Alan Flurry – University of Georgia

Scientists pave the way for enhanced detection and treatment of vascular graft infections – Science Daily

The Metabolome: The Missing Link that Binds the Microbiome with Human Health – Mike Milburn – GenEngNews

Proceed with caution: The Key to Reversing Autism May Be in the Microbiome – Emeran Mayer – Big Think

Microbes on the market

Carmel biotech firm scores major deal with pharmaceutical giant – Indianapolis Business Journal

Mawi DNA Technologies Launches ISWAB-Microbiome Sample Collection System – BusinessWire

Science, publishing, and career

Beware! Academics are getting reeled in by scam journals – The number of predatory publishers is skyrocketing – and they’re eager to pounce on unsuspecting scholars – Alex Gillis