Category Archives: Human oral

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

February 9, 2017

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Metabolomic analysis to determine affects of antibiotic treatment on the microbiome, capsular polysaccharide structure from marine bacterium, altering soil bacterial communities from use of organic-inorganic fertilization, new CRISPR-Cas systems discovered in uncultivated microbes.

General microbiome

Metabolic effects of Lactobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial – Reza Mobini – Diabetes, Obesity and Metabolism

Pregnancy and early life

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLOS ONE

Human oral microbiome

Isolation and identification methods of Rothia species in oral cavities – Osamu Tsuzukibashi – Journal of Microbiological Methods

Association of oral microbiome with type 2 diabetes risk – J Long – Journal of Periodontal Research

Human skin microbiome

Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin-resistant Staphylococcus aureus – Ming-Shan Kao – Biotechnology Journal

Human gut microbiome

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLOS ONE

Rett Syndrome: A Focus on Gut Microbiota – Elisa Borghi – International Journal of Molecular Sciences

Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia – Rachel V Purcell – PLOS ONE

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke – Kazuo Yamashiro – PLOS ONE

Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

Animal experiments

* Early life antibiotic exposure affects pancreatic islet development and metabolic regulation – Jiaying Li – Scientific Reports

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T Harach – Scientific Reports

Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics – AM Tarnecki – Journal of Applied Microbiology

Plant, root, and soil microbiome

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts – Monika A Gorzelak – Molecular Ecology

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLOS ONE

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations – Fang Li – Frontiers in Microbiology

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds – Renato Nallin Montagnolli – Environmental Toxicology and Pharmacology

Chapter: Phytostimulation and Biocontrol by the Plant-Associated Bacillus amyloliquefaciens FZB42: An Update – Rainer Borriss – Bacilli and Agrobiotechnology

Chapter: New Insights in Plant-Associated Paenibacillus Species: Biocontrol and Plant Growth-Promoting Activity – Sadhana Lal – Bacilli and Agrobiotechnology

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones – Sihang Yang – Frontiers in Microbiology

Water and extremophile microbiome

The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp. – Tamar L. Goulet – PLOS ONE

* Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H – Angela Casillo – Antonie van Leeuwenhoek

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Bacterial communities in sediment of a Mediterranean Marine Protected Area – Valentina Catania – Canadian Journal of Microbiology

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

The effect of top-predator presence and phenotype on aquatic microbial communities – Karen E. Sullam – Ecology and Evolution

Metabolomics

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions – Jocelyn M. Choo – mSphere

Techniques

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

More microbes

* New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements – D Richard – Molecular Ecology

Microbes in the news

Microbial Molecules from the Multitudes within Us – Matthew R. Redondo – Cell Metabolism

Boston Children’s Hospital and uBiome to Investigate Premature Births – PRWeb

Cholera bacteria stab and poison enemies at predictable rates – Georgia Institute of Technology – ScienceDaily

ADA funds Kostic Lab to create model linking the microbiome to type 1 diabetes – EurekAlert

February 4, 2017

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Today: articles on the nutrient niches that exist in the gut, how bifidobacterium might be functioning as a probiotic, and probiotic treatment in Bactrocera cucurbitae (melon fly), and astronaut’s gut bacteria in flight.

General microbiome

Effect of fermentation temperature on hydrogen production from xylose and the succession of hydrogen-producing microflora – Chunsheng Qiu – Journal of Chemical Technology and Biotechnology

Dental and periodontal health, and microbiological and salivary conditions in patients with or without diabetes undergoing haemodialysis – Gerhard Schmalz – International Dental Journal

Human gut microbiome

Microbial nutrient niches in the gut – Fátima C. Pereira – Environmental Microbiology

MicroRNAs at the epicenter of intestinal homeostasis – Antoaneta Belcheva – BioEssays

Oscillospira and related bacteria – From metagenomic species to metabolic features – Uri Gophna – Environmental Microbiology

Association between small-intestinal bacterial overgrowth and deep vein thrombosis in patients with spinal cord injuries – X. Cheng – Journal of Thrombosis and Haemostasis

Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron – Nathan D. Schwalm III – Molecular Microbiology

Animal experiments

Malondialdehyde epitopes are sterile mediators of hepatic inflammation in hypercholesterolemic mice – Clara Jana-Lui Busch – Hepatology

Time- and strain-specific downregulation of intestinal EPAS1 via miR-148a by Bifidobacterium bifidum – Amel Taibi – Molecular Nutrition and Food Research

Animal microbiome

Enhanced fitness of a Bactrocera cucurbitae genetic sexing strain based on the addition of gut-isolated probiotics (Enterobacter spec.) to the larval diet – Mingyan Yao – Entomologia Experimentalis et Applicata

Water and extremophile microbiome

Chemotype diversity in Planktothrix rubescens (cyanobacteria) populations is correlated to lake depth – Danka Haruštiaková – Environmental Microbiology Reports

Genomic and physiological analyses of ‘Reinekea forsetii’ reveal a versatile opportunistic lifestyle during spring algae blooms – Burak Avcı – Environmental Microbiology

Techniques

DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes – Lemian Liu – Molecular Ecology Resources

Microbes in the news

Change in astronaut’s gut bacteria attributed to spaceflight

Oral dose of phage cocktail prevents infection and cholera-like symptoms in animal model

UNH researchers ID bacteria contaminating seafood

Tap Water Free of Diarrhea-Causing Bacteria: Pittsburgh Mayor

Science in the News series kicks off with ‘Big Bacteria, Big Pharma, Big Problems’

Salicylic acid promotes nasal mucosa colonization by Staphylococcus aureus

January 29, 2017

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A post on fecal transplats, the gut microbiome of cranes, fungal diversity of soils, and much more.

Events and Jobs

Assistant Professor of Microbiology, Immunology & Tropical Medicine at George Washington University

General microbiome

The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier – Roni Nowarski – Cell

Effect of adsorbants on in vitro biohydrogenation of 22:6n-3 by mixed cultures of rumen microorganisms – Marlene Escobar – Animal

Pregnancy and early life

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants – Brandie D. Wagner – PLoS One

Mode of Delivery and Its Influence on the Acquisition of Streptococcus mutans in Infants – Ritu G. Ubeja – International Journal of Clinical Pediatric Dentistry

Human gut microbiome

Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine – Wolfgang Stremmel – PLoS One

Challenges in Fecal Donor Selection and Screening for Fecal Microbiota Transplantation: A Review – Michael H. Woodworth – Gut Microbes

Animal experiments

Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice – Ho Tsoi – Journal of AGA Institute: Gastroenterology Special Issure

Animal microbiome

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China – Guanghong Zhao – Wiley

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters – Hooman Derakhashani – Frontiers in Microbiology

Effect of antibiotic on survival and development of Spodoptera litura (Lepidoptera: Noctuidae) and its gut microbial diversity – Abhinay Thakur – Bullitin of Entomological Research

Plant, root, and soil microbiome

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Journal of Microbiology

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction – Stephanie G. Hays – Journal of Biomedical Engineering

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana – Rosalina García-Suárez – Journal of Applied Microbiology

Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds – Sarah Zerbs – Protein Science

Water and extremophile microbiome

Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities – Jonathan S McQuillan – Current Opinion in Biotechnology

Probiotics / prebiotics

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept – Vera Slomka – Wiley

Microbes in the news

Rebalancing gut microbiome lengthens survival in mouse model of ALS

What We’ve Learned From Studying Microbiomes

Microbiota Transfer Therapy Could Help Children With Autism

Bacteria’s sneaky way to spread by getting you to eat more

Studies show prevalence of multi-drug resistant bacteria in China

Researchers discover molecule that could fight ‘superbug’ bacteria

Microbes on the market

New Market Analysis: The global clinical microbiology market is projected to reach USD 5.77 Billion by 2021

Bacteria Hysteria

SHOCKING: You won’t BELIEVE how many GERMS are on your hands

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 20, 2017

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Infant formula with prebiotics and probiotics, acne vulgaris and staphylococcus, IBD and anti-CTLA-4 connected to the flora, protein kinase C δ and prebiotic required to strengthen intestinal epithelial barrier function. 

Events and jobs

Postdoctoral position in immunology to study host-gut microbiota interactions– University of Arizona

Research Engineer in Microbiology– l’Oréal

MICROBIOLOGY SUPERVISOR– via a Large US Medical Device company in Limerick

General microbiome

*A Review: The human microbiome and cancer-Seesandra V Rajagopala-AARC Publications

Pregnancy and early life

Oral Microbiota in Infants Fed a Formula Supplemented with Bovine Milk Fat Globule Membranes – A Randomized Controlled Trial– Niklas Timby- PLoS One

Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients– Sebastien Boutin- Molecular and Cellular Pediatrics

Early Benefits of a Starter Formula Enriched in Prebiotics and Probiotics on the Gut Microbiota of Healthy Infants Born to HIV+ Mothers: A Randomized Double-Blind Controlled Trial-Peter Cooper- Clinical Medicine Insights: Pediatrics

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

Oral Microbiota

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities-Anna Vesty- PLuS One

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

Human respiratory microbiome

*Review: Microbiomes in respiratory health and disease: An Asia-Pacific perspective– Sanjay H. Chotirmall- Official Journal of the Asian Pacific Society of Respirology

Human skin microbiome

The Role of Cutaneous Microbiota Harmony in Maintaining a Functional Skin Barrier-Hilary Baldwin- Journal of Drugs in Dermatology

Skin microbiome and acne vulgaris: staphylococcus, a new actor in acne– Brigitte Dreno- Experimental Dermatology

Human vaginal microbiome

Subclinical Alteration of the Cervical-Vaginal Microbiome in Women with Idiopathic Infertility– Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Intestinal Bacteria Composition and Translocation of Bacteria in Inflammatory Bowel Disease– Spyros Vrakas- PLoS One

*Review- The Gastrointestinal Tract as a Key Target Organ for the Health-Promoting Effects of Dietary Proanthocyanidins– Maria Jose Cires- frontiers in Nutrition

Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration– Martin S. Zinkernagel- Scientific Reports

*Review: Inflammatory bowel disease and cancer response due to anti-CTLA-4: is it in the flora?-Franck Carbonnel- Seminars in immunopathology

Animal experiments

ZiBuPiYin recipe improves cognitive decline by regulating gut microbiota in Zucker diabetic fatty rats– Gu Chunyan – Oncotarget

Animal microbiome

Unique Bacteria Community Composition and Co-occurrence in the Milk of Different Ruminants– Li Zhipeng- Scientific Reports

Plant, root, and soil microbiome

Mycorrhizal specificity does not limit the distribution of an endangered orchid species- Michael Waud – Molecular Ecology

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts– Monika A. Gorzelak- Molecular Ecology

Probiotics / prebiotics

Protein kinase C δ signaling is required for dietary prebiotic-induced strengthening of intestinal epithelial barrier function– Richard Y. Wu- Scientific Reports

Antioxidant properties and global metabolite screening of the probiotic yeast Saccharomyces cerevisiae var. boulardii– Suprama Datta- Journal of the Science of Food and Agriculture

Bioinformatics

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons– Illias Lagkouvardos- PeerJ

Microbes on the market

FishTaco: Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome– Ohad Manor

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 12, 2017

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uBiome blog

Losing Weight is the Most Popular New Year’s Resolution – Could Probiotics Help? – Julie Taylor – uBiome

Video: Young Microbiome Researchers: Celsius & Beyond – uBiome
For the uBiome team, working with other scientists is always rewarding, but we particularly enjoyed our recent collaboration with a team of researchers, many of whom were swamped by their lab coats and blue nitrile gloves.

Jobs

Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Pregnancy and early life

* A molecular portrait of maternal sepsis from Byzantine Troy – Alison M Devault – eLIFE

The Generation R Study: design and cohort update 2017 – Marjolein N. Kooijman – European Journal of Epidemiology

Human oral microbiome

On the ecosystemic network of saliva in healthy young adults – Egija Zaura – The ISME Journal

Human gut microbiome

Seven brief reviews: Topical Issue of the Journal of Immunology: The Macro Influence of the Microbiome – Pamela J. Fink – The Journal of Immunology

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

Animal experiments

Neuroblastoma causes alterations of the intestinal microbiome, gut hormones, inflammatory cytokines, and bile acid composition – Christoph Castellani – Pediatric Blood & Cancer

Routine assessment of the gut microbiome to promote preclinical research reproducibility and transparency – Hannah R Wardill – Gut

Animal microbiome

Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves – Tadashi Takino – Journal of Veterinary Medical Science

Population- and growth-related differences in helminthic fauna of finless porpoises (Neophocaena asiaeorientalis) in five Japanese populations – Akira Shiozaki – Journal of Veterinary Medical Science

Antifeedants Produced by Bacteria Associated with the Gut of the Pine Weevil Hylobius abietis – Karolin Axelsson – Microbial Ecology

Plant, root, and soil microbiome

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel – Binu M. Tripathi – Microbial Ecology

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil – Eoin Gunnigle – Scientific Report

Foliar application of the leaf-colonizing yeast Pseudozyma churashimaensis elicits systemic defense of pepper against bacterial and viral pathogens – Gahyung Lee – Scientific Reports

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes – Joana P. Fernandes – Science of the Total Environment

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics – Diogo A.M. Alexandrino – Science of the Total Environment

* Redox conditions and marine microbial community changes during the end-Ordovician mass extinction event – Justyna Smolarek – Global and Planetary Change

Use of plant growth promoting bacterial strains to improve Cytisus striatus and Lupinus luteus development for potential application in phytoremediation – María Balseiro-Romero – Science of the Total Environment

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes -Joana P. Fernandes – Science of the Total Environment

Communication of Sedentary Plant-Parasitic Nematodes With Their Host Plants – T. Hewezi – Advances in Botanical Research

Book chapter: Application of Microbiology in Dryland Agriculture – Minakshi Grover – Innovations in Dryland Agriculture

Water and extremophile microbiome

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments – Karen A. Cameron – Microbial Ecology

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring – Laura Ward – The ISME Journal

* Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics – Abraham G. Moller – PeerJ

Abundance of microorganisms and enzyme activity in the rapids-pool-benchland systems in natural Douliu River of China – Zhen Hong Wang – PeerJ Preprint

Distinct sensitivity of fungal freshwater guilds to water quality – Oliver Röhl – Mycological

Food microbiology

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses – Jing Li – BMC Microbiology

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation – Peter R Sternes – bioRxiv

Waste and pollution microbiology

Microbial community structure in a full-scale anaerobic treatment plant during start-up and first year of operation revealed by high-throughput 16S rRNA gene amplicon sequencing – Else Marie Fykse – Bioresource Technology

Bioinformatics

* MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes – Wei Ma – Scientific Reports

Microbial ecology

Review: Where less may be more: how the rare biosphere pulls ecosystems strings – Alexandre Joussett – ISME Journal

Microbes in the news

Gut science is radically changing what we know of the human body – Pat Rich – University Affairs Canada

Renowned microbiology expert to visit West Florida. Claire Fraser will present, “The Human Gut Microbiome in Health and Disease” – SR Press Gazette

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Researchers develop new compound to fight cytomegalovirus – EurekAlert

Eating red meat six times a week could increase chances of getting painful bowel disease – Daisy Dunne – Mirror

This looks intriguing: Microbiota and the masses: a love story – S. B. Divya – MacMillan

Microbes on the market

Gut microbiome profiling tests propelled by customer demand – Vijay Shankar – Nature Biotechnology

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business

Bik’s non-microbiology picks

UCSF Receives Historic Half-Billion-Dollar Donation – Lindsey Hoshaw – KQED

This is a tragic/comic read, but note that the original post contained some offending language, that was removed after protests on e.g. Twitter. The Rise and Fall of a Shrimp Biologist – David Scholnick – Scientific American

January 8, 2017

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Human mouth microbiome

Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections – Hila Mizrahi – Scientific Reports

Human reproductive tract microbiome

Investigation of the microbiota of the reproductive tract in women undergoing a total hysterectomy and bilateral salpingo-oopherectomy – Shana M. Miles – Fertility and Sterility

Human skin microbiome

Review: Performing Skin Microbiome Research: A Method to the Madness – Heidi H. Kong – Journal of Investigative Dermatology

Human gut microbiome

Sleeve gastrectomy drives persistent shifts in the gut microbiome – Cyrus Jahansouz – Surgery for Obesity and Related Diseases

Review: Gut microbiota in vascular disease: Therapeutic target? – Anbazhagan AN – Current Vascular Pharmacology

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

Reviews in Gastroenterology Clinics of North America
Diet and the Microbiome – Nida Murtaza
The Gut Microbiota in Inflammatory Bowel Disease – Donal Sheehan
The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan
Biology of the Microbiome : Interactions with the Host Immune Response – Sylwia Smolinska
Biology of the Microbiome 2: Metabolic Role – Jia V. Li

Animal experiments

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome – Nicolaas H Fourie – Gut Microbes

Animal microbiome

Greater Species Richness of Bacterial Skin Symbionts Better Suppresses the Amphibian Fungal Pathogen Batrachochytrium Dendrobatidis – Jonah Piovia-Scott – Microbial Ecology

Plant, root, and soil microbiome

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters – Riegardt M. Johnson – Extremophiles

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere – Adil Essarioui – Microbial Ecology

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency – Hyunjun Cho – Microbial Ecology

Water and extremophile microbiome

Effect of salinity on mercury methylating benthic microbes and their activities in Great Salt Lake, Utah – Eric S. Boyd – Science of the Total Environment

Waste and pollution microbiology

Low temperature MBBR nitrification: Microbiome analysis – Bradley Young – Water Research

Microbes in space

MELiSSA the minimal biosphere: Human life, waste and refuge in deep space – Jeremy Walker – Future

Metabolomics

Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Bioinformatics

An Informative Approach on Differential Abundance Analysis for Time-course Metagenomic Sequencing Data – Dan Luo – Bioinformatics

Microbial ecology

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber – ISME Journal

Microbes in the news

Life after death: the science of human decomposition – Mo Costandi

Japan’s fantastic emerald green algae. These great balls of fuzz, look lovely, are zero maintenance and keep water clean – James Wong

Cavities Are Contagious: Kissing And 3 Other Ways Harmful Bacteria Spreads And Causes Tooth Decay – Lizette Borreli – Medical Daily

Same bacteria found in Indian River Lagoon killed 10 in Florida in 2016 | Map – Tyler Treadway – TC Palm

Wake up, wipe out: How oxygen can help take down antiobiotic-resistant bacteria – Cordis

Your child’s microbiome, and why its health matters – Jennifer Graham – The Washington Times

January 3, 2017

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Denture microbiome, insulin resistance and appendix microbiome in obesity, raw milk microbiome, subtropical forest soils, biofilms in drinking water systems, metabolomics of a Mediterranean diet, cell shape and biofilms.

Human oral microbiome

* The Denture-Associated Oral Microbiome in Health and Stomatitis – Baochen Shi – mSphere

Commentary: A novel strategy for diagnosing viral versus bacterial infection: implications for oral diseases – Nataly Kravchenko-Balasha – Oral Diseases

Human gut microbiome

*  Insulin resistance is associated with specific gut microbiota in appendix samples from
morbidly obese patients – Isabel Moreno-Indias – American Journal of Translational Research

Microbiology of nearly sterile sites

Improving molecular diagnosis of neonatal septicaemia: Comparative evaluation of different protocols for extraction of bacterial and fungal DNA from blood samples – Gargi Dangre-Mudey – International Journal of Current Research in Medical Sciences

Animal microbiome

* Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study – Conor J. Doyle – Applied and Environmental Microbiology

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula – Maren Ziegler – Journal of Biogeography

Plant, root, and soil microbiome

Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site – Chao Wang – Mycorrhiza

Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest – Merlin Sheldrake – New Phytologist

Modeling of mineral nutrient uptake of spruce tree roots as affected by the ion dynamics in the rhizosphere: Upscaling of model results to field plot scale – H. Nietfeld – Ecological Modelling

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

 

* Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils – Qian Zhao – Biology and Fertility of Soils

Cultivable bacterial communities associated with roots of rose-scented geranium (Pelargonium graveolens) with the potential to contribute to plant growth – Thais Freitas da Silva – Applied Soil Ecology

Isolation of Soil and Endophytic Fungi from Rice (Oryza sativa L.) – Thianrat Leewijit – Journal of Agricultural Technology

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition – A. Blaud – Advances in Agronomy

Book chapter: The Significance of Plant-Associated Microbial Rhizosphere for the Degradation of Xenobiotic Compounds – Durgesh Kumar Jaiswal – Plant Responses to Xenobiotics

Review: Plant Communication With Associated Microbiota in the Spermosphere, Rhizosphere and Phyllosphere – P. Lemanceau – Advances in Botanical Research

Review: Plant growth promoting Rhizobacteria: Biocontrol potential for pathogens – Roomina Mazhar – Pure Appl Biol

Water and extremophile microbiome

* Spatial and temporal analogies in microbial communities in natural drinking water biofilms – I. Douterelo – Science of The Total Environment

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments – Rituja Saxena – Frontiers in Microbiology

Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats – Hui Shen – Journal of Experimental Marine Biology and Ecology

Review: Biotechnological Applications of Marine Enzymes From Algae, Bacteria, Fungi, and Sponges – S. Parte – Advances in Food and Nutrition Research

Waste and pollution microbiology

Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment – Cabrol Léa – Journal of Microbiological Methods

Effect of various chemical oxidation agents on soil microbial communities – Eva Kakosová – Chemical Engineering Journal

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics – N.L. Fahrenfeld – Science of the Total Environment

Changes in the microbial community during bioremediation of gasoline-contaminated soil – Aline Jaime Leal – Brazilian Journal of Microbiology

Performance and microbial communities of completely autotrophic denitrification in a bioelectrochemically-assisted constructed wetland system for nitrate removal – Dan Xu – Bioresource Technology

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors – Marc A. Demeter – Bioresource Technology

Review: Resource recovery from wastewater by biological technologies: opportunities, challenges and prospects – Daniel Puyol – Frontiers in Microbiology

Fungi

A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance – Mary Augustina Egbuta – Advances in Microbiology

Phages

Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology – Jasna Rakonjac – Frontiers in Microbiology

Metabolomics

* Adherence to a Mediterranean diet influences the fecal metabolic profile of microbial-derived phenolics in a Spanish cohort of middle-age and older people – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemistry

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics – Adam Hunter – Metabolomics

More microbiology

* Cell morphology drives spatial patterning in microbial communities – William P. J. Smith – PNAS

Microbes in the news

A Gut Makeover for the New Year – Roni Caryn Rabin – The New York Times

Keys plan field trial for bacteria-infected mosquitoes – Associated Press

Salmonella bacteria threatens Mudumalai: cattle and elephants died – Times of India

How your gut’s circadian rhythm affects your whole body – Richard G. “Bugs” Stevens – The Conversation

Eat Dirt… It’s Good For You (So Are Worms) – Tanya Mead – The Alternative Daily