March 23, 2017

Posted on March 23, 2017 by TinaS

Today’s digest has quite a few papers in the human oral and gut microbiome with many interesting papers as the one from M. Lepczyńska addressing positive aspects of various diets on gut microbiota and its fight with parasites. In ‘Water microbiome’ you can take a look at Raquel S. Peixoto’s paper and beneficial microbes maintaining coral health, while in ‘Microbes in News’ you can read how team from Korea is tackling one of medicine’s most pressing problems – antibiotic resistance by using bacteria to fight bacteria.

General microbiome

Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation – Ling Ling Chua -Microbiome

Pregnancy and early life

Manipulating the baby biome: What are the issues? – Lai-yang Lee – Australian and New Zealand Journal of Obstetrics and Gynaecology (ANZJOG)

Ex vivo infection of human placental chorionic villi explants with Trypanosoma cruzi and Toxoplasma gondii induces different Toll-like receptor expression and cytokine/chemokine profiles – Christian Castillo – American Journal of Reproductive Immunology (AJRI)

First foods and gut microbes – Martin F. Laursen – Frontiers in Microbiology

Reproductive microbiomes a new thread in the microbial network – Michael L. Power – Reproductive Sciences

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

Human Oral

Differential responses of human dendritic cells to metabolites from the oral/airway microbiome – K. Whiteson – Clinical & Experimental Immunology

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Probiotic Lactobacillus reuteri has antifungal effects on oral Candida species in vitro – Mette Rose Jørgensen – Journal of Oral Microbiology

Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries – J-L. C. Mougeot – Journal of Oral Microbiology

Oral microbiome in HIV-associated periodontitis – Noguera-Julian – Medicine

Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome – Szymon P. Szafrański – BMC Genomics

Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Jôice Dias Corrêa – Microbiome
Human nearly-sterile sites

Alterations in gastric microbiota after H. Pylori eradication and in different histological stages of gastric carcinogenesis – Tung Hiu Li – Scientific Reports

Human gut microbiome

Oral iron supplementation: Potential implications for the gut microbiome and metabolome in patients with CKD – Guus A. M. Kortman – Hemodialysis International

Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut – Ziena Elsawi – Microbiology Open

Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini – Nature Reviews Gastroenterology & Hepatology

*Review: Blastocystis: how do specific diets and human gut microbiota affect its development and pathogenicity? – M. Lepczyńska – European Journal of Clinical Microbiology & Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLOS One

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick H. Bradley – Microbiome

Animal experiments

Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development – Dirkjan Schokker – BMC Genomics

Effects of dietary administration of Shewanella xiamenensis A-1, Aeromonas veronii A-7, and Bacillus subtilis, single or combined, on the Grass Carp (Ctenopharyngodon idella) intestinal microbiota – Kai Hao – Probiotics and Antimicrobial Proteins

Plant, root, and soil microbiome

Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L. – Munusamy Madhaiyan – Antonie van Leeuwenhoek

The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu -Sceintific Reports

Compositional stability of the bacterial community in a climate-sensitive sub-Arctic peatland – James T. Weedon – Frontiers in Microbiology

Antibiotic and heavy metal tolerance of some indigenous bacteria isolated from petroleum contaminated soil sediments with a study – Jai Godheja – International Journal of Current Microbiology and Applied Science (IJCMAS)

Water and extremophile microbiome

Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge – Ren-Mao Tian – mSystems

Impact of hypoxia on gene expression patterns by the human pathogen, Vibrio vulnificus, and bacterial community composition in a North Carolina estuary – Britney L. Phippen – Geohealth

Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments – T. Hoshino – Letters in Applied Microbiology

Phytoplankton species richness, evenness, and production in relation to nutrient availability and imbalance – Sirpa Lehtinen – Limnology and Oceanography

Metagenomic and culture-dependent analysis of the bacterial diversity of a hot spring reservoir as a function of the seasonal variation – B. A. Kikani – International Journal of Environmental Research

Beneficial microorganisms for corals (BMC): Proposed mechanisms for coral health and resilience – Raquel S. Peixoto – Frontiers in Microbiology

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research – R. K. Salis – Scientific Reports

Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers – Simon Le Bloa – PLOS One

Molecular insights on dissolved organic matter transformation by supraglacial microbial communities – Runa Antony – Environmental Science & Technology

An alternative polysaccharide uptake mechanism of marine bacteria – Greta Reintjes – ISME Journal

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments – Sophie L. Nixon – Biogeosciences

Different bacterial communities involved in peptide decomposition between normoxic and hypoxic coastal waters – Shuting Liu – Frontiers in Microbiology

Temperature- and size-scaling of phytoplankton population growth rates: Reconciling the Eppley curve and the metabolic theory of ecology – Colin T. Kremer – Limnology and Oceanography

Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient – Huabing Li – Limnology and Oceanography

Built environment

Short-term effects of great cormorant droppings on water quality and microbial community of an artificial agricultural reservoir – Il Han – Journal of Environmental Quality

Probiotics / prebiotics

Review: Gut microbiota and bacterial translocation in digestive surgery: the impact of probiotics – Shunichiro Komatsu – Langenbeck’s Archives of Surgery

Techniques

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach – Bonnie L. Brown – Gigascience

Microbes in the news

Diabetes patients can lower blood sugar through gut bacteria; fecal microbes found to have curative properties – The Science Times

Predatory bacteria as a new ‘living’ antibiotic -Phys Org

Achievements of the human microbiome project – News Medical Life Sciences

Warning: current ecological microbiome may be on the verge of disaster due to antibiotics – Nature World News

March 22, 2017

Posted on March 22, 2017 by Anitha Isaiah

Today’s digest features interesting review articles on the role of microbiome in health and disease, heart failure, and how the respiratory tract microbiota act as gatekeepers to respiratory health. Also, we have original research articles on the response of bacterial communities in oil-contaminated marine waters to addition of chemical and biological dispersants. Also, a very fascinating article in Harvard Business review on the gender bias against junior female scientists. Not surprising!! Enjoy.

General microbiome

*Review: The role of the microbiome in human health and disease: an introduction for clinicians – Vincent B Young – British Medical Journal

*Review: Targeting the Microbiome in Heart Failure – Allyson Zabell – Current Treatment Options in Cardiovascular Medicine

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – Guoqin Yu – international Journal of Cancer

Pregnancy and early life

Late preterm birth has direct and indirect effects on infant gut microbiota development during the first six months of life – M Forsgren – Acta Pediatrica

Vaginal microbiome

Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women – Vladimir V. Demkin – Anaerobe

Human oral microbiome

Changes in salivary microbiota increase volatile sulfur compounds production in healthy male subjects with academic-related chronic stress – Bruno Dias Nani – Plos One

Candida albicans biofilm heterogeneity does not influence denture stomatitis but strongly influences denture cleansing capacity – Lindsay E. O’Donnell – Journal of Medical Microbiology

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human respiratory microbiome

*The microbiota of the respiratory tract: gatekeeper to respiratory health – Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Editorial : Infant colic is still a mysterious disorder of the microbiota–gut–brain axis – Anna Pärtty – Acta Pediatrica

Review: More Flavor for Flavonoid-Based Interventions? – Nadeem O. Kaakoush – Trends in Molecular Medicine

Perspectives : New Frontiers in Fibers: Innovative and Emerging Research on the Gut Microbiome and Bone Health – Taylor C. Wallace – Journal of the American College of Nutrition

Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology? – Monika Adamczyk-Sowa – Journal of Immunology Research

The Role of Intestinal Alkaline Phosphatase in Inflammatory Disorders of Gastrointestinal Tract – Jan Bilski – Mediators of Inflammation

The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension – Ruth A. Riedl – Current Hypertension Reports

Fecal Microbiota Transplantation

Commentary: A proposed definition of microbiota transplantation for regulatory purposes – Diane E. Hoffmann – Gut Microbes

Review: Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature – Nathaniel Aviv Cohen – Digestive Diseases and Sciences

Animal microbiome

Review: Role of the microbiome in swine respiratory disease – Megan C. Niederwerder – Veterinary Microbiology

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows – William M. Sischo – Journal of Dairy Science

Comparative analysis of fecal microbial communities in cattle and Bactrian camels – Liang Ming – Plos One

Sheep fed with banana leaf hay reduce ruminal protozoa population – Cláudio Eduardo Silva Freitas – Tropical Animal Health and Production

Metabolomics

Review: Metabolomic-guided discovery of Alzheimer’s disease biomarkers from body fluid – Che Nor Adlia Enche Ady – Journal of Neuroscience Research

Animal experiments

The farming environment protects mice from allergen-induced skin contact hypersensitivity – C. P. Frossard – Clinical and Experimental Allergy

Metabolomics insights into diabetes nephropathy and protective effects of Radix Scutellariae on rats using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry – Lihui Men – RSC Advances

Plant, root, and soil microbiome

Root plant growth promoting rhizobacteria inoculations increase ferric chelate reductase (FC-R) activity and Fe nutrition in pear under calcareous soil conditions – Muzaffer İpek – Scientia Horticulturae

Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France) – Jorge R. Osman – Rhizosphere

Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands – Cuiping Zhang – Environmental Science and Pollution Research

Water and extremophile microbiome
Characterization of spatial distribution of the bacterial community in the South Sea of Korea – Ji-Hui Seo – Plos One

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs – Ping Kong – Plos One

*Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants – Camila Rattes de Almeida Couto – Journal of Environmental Management

Probiotics / prebiotics

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation – W. Fonseca- Mucosal Immunology

Identification of the key excreted molecule by Lactobacillus fermentum related to host iron absorption – Ana González – Food Chemistry

Effect of 8-weeks prebiotics/probiotics supplementation on alcohol metabolism and blood biomarkers of healthy adults: a pilot study – Christopher Irwin – European Journal of Nutrition

Bioinformatics

Making big data smart—how to use metagenomics to understand soil quality – Gisle Vestergaard – Biology and Fertility of Soils

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – Monika Balvočiūtė – BMC Genomics

Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys – Sofie Thijs – Frontiers in Microbiology

Microbes in the news

Asthma: Researchers discover how exposure to microbes protects against asthma

Rainy Day? Microbes May Be at Play

Building A Brewery, Chapter 4: For the Love of Microbes

Science, publishing, and career

*Junior Female Scientists Aren’t Getting the Credit They Deserve “despite evidence that women on average, may perform better than men in early stage of their careers”

Anitha’s non-microbiology picks

How Pluto’s haze could explain its red spots

Cancer cells cast a sweet spell on the immune system

Actinide chemistry expands to new oxidation states

March 21, 2017

Posted on March 21, 2017 by Kiran

Events and jobs

Microbiology Department Manager – Medlab Pathology – Sydney

General microbiome

The ecology of human microbiota: dynamics and diversity in health and disease – A Karkman – Annals of the New York Academy of Sciences

Human gut microbiome

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

Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health – DR Covian – Frontiers in Microbiology

Animal microbiome

Effects of a protected inclusion of organic acids and essential oils as antibiotic growth promoter alternative on growth performance, intestinal morphology and gut microflora in broilers – Y Liu – Animal Science Journal

Extreme drought, host density, sex, and bullfrogs influence fungal pathogen infection in a declining lotic amphibian – AJ Adams – Ecosphere

Neoagarotetraose protects mice against intense exercise-induced fatigue damage by modulating gut microbial composition and function – N Zhang – Molecular Nutrition and Food Research

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Die – L Zhang – Scientific Reports

Plant, root and soil microbiome

*Review: Rhizogenic agrobacteria in hydroponic crops: epidemics, diagnostics and control – L Bosmans – Plant Pathology

Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria – K Tsuji – Plant, Cell and Environment

Water microbiome and extremophiles

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary – MW Smith – Microbiology Open

Metagenomics of Hyperthermophilic Environments: Biodiversity and Biotechnology – A Strazzulli – Microbial Ecology of Extreme Environments

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment – DFR Cleary – Marine Ecology

Crenarchaeal Viruses of Hot Springs: Diversity, Ecology and Co-evolution – AC Ortmann – Microbial Ecology of Extreme Environments

*Review: Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review – KD Weynberg – Viruses

Microbial Electron Transport in the Deep Subsurface – J Hinks – Microbial Ecology of Extreme Environments

New Insights into the Microbial Diversity of Polar Desert Soils: A Biotechnological Perspective – J v Dorst – Microbial Ecology of Extreme Environments

Transcriptomics

Mechanism for microbial population collapse in a fluctuating resource environment – S Turkarslan – Molecular Systems Biology

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – M Balvociute – BMC Genomics

Prediction of virus-host infectious association by supervised learning methods – M Zhang – BMC Bioinformatics

Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq) – L Krakova – International Biodeterioration & Biodegradation

More microbes

*Review: The role of bacillithiol in Gram-positive Firmicutes – P Chandrangsu – Antioxidants & Redox Signaling

The effect of antibiotics and diet on enterolactone concentration and metabolome studied by targeted and non-targeted LC-MS metabolomics – AK Bolviq – Journal of Proteome Research

Exploring the Viral Ecology of High Latitude Aquatic Systems – C Chenard – Microbial Ecology of Extreme Environments

The Nature and Relevance of Solvent Stress in Microbes and Mechanisms of Tolerance – M Manefield – Microbial Ecology of Extreme Environments

Surveillance of Exhibit Associated Aquatic Viruses Using Next Generation Sequencing Technologies – WV Bonn – IAAAM 2016

Microbes in the news

Before you consume billions of live bacteria … – E Cauthorn – Las Vegas Sun

Bacteria between humans and pets? Could improve global health: researchers – M Shah – Toronto Sun

There is a reason dogs like meat – NZ Herald

ANTIBIOTIC APOCALYPSE: Harvard reveals doomsday scenario that could KILL 10 million a year – O Smith – Express

THE ALTERATION OF THE INTESTINAL MICROBIOTA COULD PROTECT METABOLIC DISEASES – Zoe – The Quebec Times

March 18, 2017

Posted on March 18, 2017 by bergmaureen

Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 17, 2017

Posted on March 17, 2017 by TinaS

Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day.In the first highlighted paper the authors present the structural basis of the day-night transition in a cyanobacterial circadian clock. The second highlighted paper evaluated the effects of antibiotic treatment on the honeybee gut microbiome. The authors found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survival.

General microbiome

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria – Morgan M. Stanton – Small

Structural basis of the day-night transition in a bacterial circadian clock – Roger Tseng – Science

Pregnancy and early life

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location – C Gómez-Gallego – Annals of Nutrition and Metabolism

Human respiratory microbiome

Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus – RD Waite – PLOS One

Human gut microbiome

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism – Simon Nicolas – Molecular Systems Biology

Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy – Yan-Dan Ren – Hepatology

The Microbiome and Host Behavior – Vuong HE – Annual Review of Neuroscience

Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet – Zeinab Mokhtari – Advances in Nutrition

Animal experiments

Intestinal transcriptome modulation by functional diets in rainbow trout: A high-throughput sequencing appraisal to highlight GALT immunomodulation – Ana Teresa Gonçalves – Fish & Shellfish Immunology

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Diet – Li Zhang – Scientific Reports

Oral administration of synthetic porcine beta-defensin-2 improves growth performance and cecal microbial flora and down-regulates the expression of intestinal toll-like receptor-4 and inflammatory cytokines in weaned piglets challenged with enterotoxigenic Escherichia coli – Zhiru Tang – Animal Science Journal

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro – Elena Herrmann – BioMed Research International

Animal microbiome

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology

Plant, root, and soil microbiome

Accessing the Carbofuran Degradation Ability of Cultures From Natural River Biofilms in Different Environments – Chien-Jung Tien – CLEAN – Soil, Air, Water

Impact of Agri-Usable Nanocompounds on Soil Microbial Activity: An Indicator of Soil Health – Priyanka Khati – CLEAN – Soil, Air, Water

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites – Mitja N.P. Remus-Emsermann – SIGS Standards in Genomic Sciences

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites – Prem Prashant Chaudhary – Microbiology Open

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Effect of pesticides on microbial communities in container aquatic habitats – Ephantus J. Muturi – Scientific Reports

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – KI Twing – Frontiers in Microbiology

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer – Ping Zhang – Environmental Science & Technology

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment – Pauliina Rajala – Frontiers in Microbiology

Built environment

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community – Fei Pan – Scientific reports

Probiotics / prebiotics

Achieving High Yield of Lactic Acid for Antimicrobial Characterization in Cephalosporin-Resistant Lactobacillus by the Co-Expression of the Phosphofructokinase and Glucokinase – Gong Y – Journal of Microbiology and Biotechnology

Phages and viruses

Inflammation boosts bacteriophage transfer between Salmonella spp.– Médéric Diard – Science

Bioinformatics

microclass: an R-package for 16S taxonomy classification – Kristian Hovde Liland – BMC Bioinformatics

Microbes in the news

Team finds new way that bacteria lay siege to neighboring cells by hijacking two factors involved in protein synthesis – Phys.Org

March 14, 2017

Posted on March 14, 2017 by xinhuang7

A short Digest today, many news pieces, a new bioinformatics tool from the Rob Knight lab, and papers on genome-scale metabolic models.

General microbiology

Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance – Jonathan M. Stokes – Nature Microbiology

Press: Antiprotozoal drug, Pentamidine, used with antibiotics effective against ‘superbugs’: McMaster research – Outbreak News Today

Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis – Gang Luo – Environmental Science & Technology

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families – Ana Popovic – Scientific Reports

Animal experiments

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis – Huijuan Jia – Scientific Reports

Animal microbiome

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants – Jon G. Sanders – bioRxiv

Plant, root, and soil microbiome

Book chapter – Chapter 16: Growth Promotion Features of the Maize Microbiome: From an Agriculture Perspective – Ubiana de Cássia Silva – Plant-Microbe Interaction: An Approach to Sustainable Agriculture

Metabolomics

Evaluating the Capabilities of Microbial Chemical Production Using Genome-Scale Metabolic Models – Hugh M. Purdy and Jennifer L. Reed – Current Opinion in Systems Biology

Model-based quantification of metabolic interactions from dynamic microbial-community data – Mark Hanemaaijer – PLoS One

Review: Current state and applications of microbial genome-scale metabolic models – Won Jun Kim – Current Opinion in Systems Biology

Bioinformatics

Deblur: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping – Amnon Amir – mSystems

Deblur: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns – Amnon Amir – mSystems

Microbes in the news

Common Bacteria May Control Disease-Carrying Insects – Jessica Berman – VOA

Study finds new evidence that viruses and bacteria may be found in some public water supply wells – Home Town Source

Your mobile phone has more germs than a toilet seat, but should you worry? – The News Minute

Mining nature for the next groundbreaking antibiotic – Julia Franz – PRI

March 12, 2017

Posted on March 12, 2017 by galit_ms

The first day of daylight saving time in the USA and if your Sunday morning started in a (relative) darkness just read about the viruses in the oceanic basement. Then find out why yogurt can help your mood. More interesting papers about the gut-brain connection, a microbiota-centric view of diseases of the upper gastrointestinal tract, microbiome and Type 1 & 2 diabetes, and a new method of detecting bacteria during root canal treatments.

General microbiome

Review: Calling All Hosts: Bacterial Communication In Situ – Jessica L. Cleary – Chem

Gut-Brain connection

The Association Between Temperament and Microbiota in Healthy Individuals: A Pilot Study – Kim H – Psychosomatic medicine

Gut-brain actions underlying comorbid anxiety and depression associated with inflammatory bowel disease – Aine Abautret-Daly -Acta Neuropsychiatrica

Human gut microbiome

A microbiota-centric view of diseases of the upper gastrointestinal tract – Gerardo Nardone- Gastroenterology & Hepatology

Review: Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine – Jens Nielsen – Cell Metabolism

Intestinal Microbiota in Type 2 Diabetes and Chronic Kidney Disease – A. Sabatino – Current Diabetes Reports

The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins – Elsa Pinto – Microbiology

Therapeutic efficacy of oral immunization with a non-genetically modified Lactococcus lactis-based vaccine CUE-GEM induces local immunity against Helicobacter pylori infection – Wei Liu – Applied Microbiology & Biotech

Water and extremophile microbiome

Viruses in the Oceanic Basement – OD Nigro -MBio

Models

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium -Yuli Wang – Biomaterials

Built environment

Review: Microbiome involved in microbial electrochemical systems (MESs): Rijuta G Saratale- Chemosphere

Microbes in the news

Probiotic found in yogurt can reverse depression symptoms, Researchers at the University of Virginia School of Medicine finds

New method of detecting bacteria during root canal treatments

March 11, 2017

Posted on March 11, 2017 by Kiran

General microbiome

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – M Pammi – Microbiome

Is the 25 year hepatitis C marathon coming to an end to declare victory? – Khulood T Ahmed – bioRxiv

Natural antimicrobial peptide complexes in the fighting of antibiotic resistant biofilms: Calliphora vicina medicinal maggots – N Gordya – PLoS One

Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes – An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions – PM Swe – PLoS Neglected Tropical Disease

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – C Barthels – Nature Communications

Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal – I Khan – Medical Principles and Practice

Human skin microbiome

Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy

Human vaginal microbiome

*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology

Human gut microbiome

*Review: Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy – UC Ghoshal – Gut and Liver

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – H Tilg – Cell Metabolism

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

Animal microbiome

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats – Vientós-Plotts AI – PLoS One

A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – R Batacan – Journal of Applied Microbiology

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – MS Llewellyn – Scientific Reports

Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile, haemato-biochemical parameters and immune responses – A Nandi – Aquaculture Research

Plant, root and soil microbiome

Simplified and representative bacterial community of maize roots – B Niu – PNAS

Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba) – R Prior – Journal of Environmental Science and Health, Part B

Thermophilic microorganisms in arable land around medieval archaeological sites in Northern Caucasus, Russia: Novel evidence of past manuring practices – E Chernysheva – Geoarchaeology

Water and Extremophiles

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – AR Rowe – Environmental Microbiology

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – M Kwon – Environmental Microbiology

Transcriptomics and Proteomics

A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv

Techniques

Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis – L D’Amico – Lab on a Chip

A fast small-sample kernel independence test for microbiome community-level association analysis – X Zhan – Biometrics

More microbes

Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health – Leulier F – Cell Metabolism

Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa – EM Waters – Thorax

*Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Meibomian gland disease and the microbiotome: is it time for ocular probiotics? – S Watson – Clinical & Experimental Ophthalmology

*Review: Infection in Organ Transplantation – JA Fishman – American Journal of Transplantation

Azole resistance in Candida albicans from animals: Highlights on efflux pump activity and gene overexpression – MFG Rocha – Mycoses

The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae) – F Gomez – Journal of Eukaryotic Microbiology

Gut microbiota analysis in rats with methamphetamine-induced conditioned place preference – T Ning – bioRxiv

Microbes in news

What is Metagenomics? – Y Smith – News Medical

UCC researchers discover weapon to fight antibiotic resistance – D Ahlstrom – The Irish Times

Community gets an eye-opening lesson in human microbiome and our western lifestyle – C MacDonald – UToday

Microbiome Research Symposia Review: Microbiome and Diseases – J Phelan – Taconic Biosciences

Q&A with Zeus Capital’s Dr Gary Waanders: Live Biotherapeutics & 4D Pharma PLC (LON:DDDD) – A Stone – Directors Talk Interviews

Do You Have the Guts to Perform? Microbial Balance, the Brain and Athletic Performance – SJ Hewlings – Natural Products Insider

New probiotics meant to balance microbial, fungal communities in gut – H Schultz – NUTRAingredients

Google Leads $51M Investment in Startup Tackling Drug-Resistant Bacteria – R Bushey – R & D

Your bacteria-ridden makeup could be the reason you keep getting sick – A Mulvaney – Independent

March 10, 2017

Posted on March 10, 2017 by cgarrettwilson

Ancient microbial DNA in Neanderthal dental calculus; the role of fungus in inflammatory bowel disease; symbiotic bacteria in the Hawaiian bobtail squid reproductive system; and a colorimetric/electrochemical device for detection of food and waterborne bacteria.

Events and jobs
Microbiology/Immunology Faculty – West Virginia School of Osteopathic Medicine – Lewisburg, West Virginia

Pregnancy and early life
Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota – Alyssa Robinson – Journal of Pediatric Gastroenterology and Nutrition

Review: Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – Mohan Pammi – Microbiome

Human oral microbiome
New approach for studying mobile genes using metagenomic analysis – K. Ishihara – Oral Diseases

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus – Laura S. Weyrich – Nature

In the News: Prehistoric ‘Aspirin’ Found in Sick Neanderthal’s Teeth – National Geographic

Human skin microbiome
Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool – Ning Chin – ProQuest Dissertations Publishing

Human vaginal microbiome
Review: The role of the vaginal microbiome in gynecological cancer: a review – Champer M. – BJOG

Human gut microbiome
A translational investigation into the role of dietary fatty acids in modulating endotoxemia and associated inflammation – Joshua Mark Lyte – ProQuest Dissertations Publishing

Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity – Malini Ahuja – Cell Metabolism

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – Herbert Tilg – Cell Metabolism

Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification – Shuang Jin – Scientific Reports

Gut microbiota modulation of chemotherapy efficacy and toxicity – James. L. Alexander – Nature Reviews Gastroenterology & Hepatology

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – Christian Barthels – Nature Communications

Faecal microbiota transplantation in clinical practice – E M Terveer – Gut

Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder – Ruth Ann Luna – Cellular and Molecular Gastroenterology and Hepatology
Animal experiments
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – Romeo Batacan – Journal of Applied Microbiology

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Chiaro TR – Science Translational Medicine

Animal microbiome
Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen – Henk J. Van Lingen – Frontiers in Microbiology

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome
Arsenic Transport in Rice and Biological Solutions to Reduce Arsenic Risk from Rice – Yanshan Chen – Frontiers in Plant Science

Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress – Shalaka Shinde – Frontiers in Plant Science

Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups – Jingjing Peng – Frontiers in Microbiology

Fertilization of Phaseolus vulgaris with the Tunisian rock phosphate affects richness and structure of rhizosphere bacterial communities – Darin Trabelsi – Applied Soil Ecology

Bioprospecting plant-associated microbiomes – Christina A. Muller – Journal of Biotechnology

Water and extremophile microbiome
Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation – MA Jebelli – Ecotoxicology and Environmental Safety

Performance and kinetics of membrane and hybrid moving bed biofilm-membrane bioreactors treating salinity wastewater – Alejandro Rodriguez-Sanchez – AlChE Journal

Metabolomics
Technological development of high-performance MALDI mass spectrometry imaging for the study of metabolic biology – Adam D. Feenstra – ProQuest Dissertations Publishing

Food microbiology
The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products – Solimar G. Machado – Frontiers in Microbiology

Culturable microorganisms during fermentation of Veltlínske zelené (Grüner Veltliner) ice wine – K. Ženišová – Journal of Food and Nutrition Research

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Probiotics/prebiotics
Case Study: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study – Elisa Salvetti – Applied Microbiology and Biotechnology

Techniques
Colorimetric and Electrochemical Bacteria Detection Using Printed Paper- and Transparency-Based Analytic Devices – Jaclyn A. Adkins – Analytical Chemistry

Microbes in the news
Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – The New York Times

Garrett’s non-microbiology picks
‘Plan bee’ drone artificially pollinates flowers on behalf of bees – Design Boom

March 9, 2017

Posted on March 9, 2017 by anjacobson

A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Press: WATCH: Raindrops Catapult Bacteria Into The Air, And It’s Beautiful – Rae Ellen Bichell – NPR

Press: A light rain can spread soil bacteria far and wide, study finds – Environmental News Network

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

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A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Events and jobs

General microbiome

Human respiratory microbiome

Human gut microbiome

Animal experiments

Animal microbiome

Plant, root, and soil microbiome

Water and extremophile microbiome

Built environment

Techniques

Microbes in the news

Microbes on the market

Bacteria Hysteria

General microbiome

Gut-Brain connection

Human gut microbiome

Water and extremophile microbiome

Models

Built environment

Microbes in the news

General microbiome

Human skin microbiome

Human vaginal microbiome

Human gut microbiome

Animal microbiome

Plant, root and soil microbiome

Water and Extremophiles

Transcriptomics and Proteomics

Techniques

More microbes

Microbes in news