Category Archives: Metagenomics & Bioinformatics

December 21, 2017

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Today’s digest features an original research article showing administration of Bifidobacterium may ameliorate toxicity of a a checkpoint blockade antibody in mice and a review on the concept of enterotypes in the human gut microbiome.

Events and jobs

Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop at Kellogg Biological Station 24-30 June 2018.

Human respiratory microbiome

Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection – Emerging microbes & infections – Hai-feng Lu

Human gut microbiome

Review: Gut microbiota in 2017: Contribution of gut microbiota–host cooperation to drug efficacy – Nathalie M. Delzenne – Nature reviews gastroenterology & hepatology

Editorial : Are diets the answers to colon ills? Food, irritable bowel syndrome and the microbiome – Quigley Eamonn M.M.

Exposure to environmental microbiota explains persistent abdominal pain and irritable bowel syndrome after a major flood – NurFadhilah Yusof – Gut Pathogens

*Perspective : Enterotypes in the landscape of gut microbial community composition – Paul I. Costea – Nature Microbiology

Animal experiments

Evaluation of Probiotic Lactobacillus fermentum CCM 7421 Administration with Alginite in Dogs – Viola Strompfová – Probiotics and Antimicrobial Proteins

* Bifidobacterium can mitigate intestinal immunopathology in the context of CTLA-4 blockade – Feng Wang – PNAS

Plant, root, and soil microbiome

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – Shuo Jiao – Molecular ecology

Water and extremophile microbiome 

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes – Pia I. Scherer – Frontiers in Microbiology

Probiotics / prebiotics

Galactooligosaccharide supplementation provides protection against Citrobacter rodentium-induced colitis without limiting pathogen burden – Hatem Kittana – Microbiology

Bifidobacteria and Their Molecular Communication with the Immune System – Lorena Ruiz – Frontiers in Microbiology

Phages and viruses

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria – Rosalind A. Gilbert – Frontiers in Microbiology

Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking – Lesley A. Ogilvie – The ISME Journal

Pre-print: Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

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Microbes in the news

Researchers Create Bacteria-Killing Steel Nanospikes

Are phages our best bet against antibiotic-resistant bacteria?

Bacteria Art

Science and Art Join Forces to Challenge our Anthropocentric Worldviews

Loyola Biology Professor Will Display Art At ARC Gallery

Anitha’s non-microbiology picks

Scientists discover entirely new material that cannot be explained by classical physics

Smothered jet may explain weird light from neutron star crash

Study of beetle flagellum offers possible way to improve medical devices

December 20, 2017

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A long but great digest today, with lots of diversity – a few studies of poultry gut microbiome and the effects food/probiotics have, a solid showing for human gut microbiome studies – covering its implications on a range of disorders, some news about biotech companies, studies on plants and from environmental sources, a promising analysis of techniques used for sampling for human gut studies, and my normal dosage of non-microbiology science.  Happy Holidays!

Events and jobs

ON-DEMAND WEBINAR How to Harness the Microbiome: Considerations and Implications of the Microbiome in Preclinical Research with Reproducible Results

Senior Biomedical Scientist (Microbiology) – Matchtech – Essex, England

Staff Research Associate 3, UCLA Department of Microbiology, Immunology and Molecular Genetics

Assistant (10782) – Clinical chemistry, microbiology and immunology – Ghent University

Pregnancy and early life

Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice – Dagbjort H. Petursdottir – Frontiers in Immunology

[Accepted Manuscript] – The neonatal window of opportunity – early priming for life – Harald Renz -Journal of Allergy and Clinical Immunology

Human oral microbiome

The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species – Abdrazak Amer – Frontiers in Microbiology

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition – Alice Harding – Frontiers in Aging Neuroscience

Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome – Richard R. Watkins – Journal of Intensive Care Medicine

Human nearly-sterile sites

Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens – Min Xu – Transfusion

Human gut microbiome

** High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden – Ninalynn Daquigan – npj Biofilms and Microbiomes

Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus – C. David Owen – Nature Communication

[Editorial] Is gut microbiome a predictive marker to response to immune checkpoint inhibitors? – Khalil Saleh – Immunotherapy

* Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis – Ran Huo – Front. Cell. Infect. Microbiology

Possible role of the gut microbiota–brain axis in the antidepressant effects of (R)-ketamine in a social defeat stress model – Chun Yang – Translational Psychiatry

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria – Kathryn A. Knoop – Science Immunology

* Stool Donor Body Mass Index Does Not Affect Recipient Weight After a Single Fecal Microbiota Transplantation for C. difficile Infection – Monika Fischer – Clinical Gastroenterology and Hepatology

The role of microbiota in the pathogenesis of schizophrenia and major depressive disorder and the possibility of targeting microbiota as a treatment option – Fengli Lv – Oncotarget

Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota – Fengping Liu – Oncotarget

Animal experiments 

* Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice – Xiaomeng You – npj Science of Food

Significant improvement of intestinal microbiota of gibel carp (Carassius auratus gibelio) after traditional Chinese medicine feeding – Zhenbing Wu – Journal of Applied Microbiology

* The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review – Viviana Clavijo – Poultry Science

Influence of dietary avilamycin on ileal and cecal microbiota in broiler chickens – J-H Choi – Poultry Science

Plant, root, and soil microbiome

* Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale – Pauline Bernardo – The ISME Journal

Dispersal alters bacterial diversity and composition in a natural community – Michaeline B N Albright – The ISME Journal

** Genomic features of bacterial adaptation to plants – Asaf Levy – Nature Genetics

Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area – Liang Xue – Frontiers in Microbiology

First insight into microbial community composition in a phosphogypsum waste heap soil – Sylwia Zielińska – ABP

* Harnessing the microbiomes of Brassica vegetables for health issues – Birgit Wassermann – Scientific Reports

Water and extremophile microbiome 

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria – Stefan M Neuenschwander – The ISME Journal

Recurrent patterns of microdiversity in a temperate coastal marine environment – Meghan Chafee – The ISME Journal

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium – Robbie M. Martin – PLOS One

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste – Valeria Ventorino – Waste Management

Food microbiology

* Inner Workings: Companies seek food safety using a microbiome approach – Carolyn Beans – PNAS

Phages and viruses

* Temporal dynamics of uncultured viruses: a new dimension in viral diversity – Ksenia Arkhipova – The ISME Journal

Bioinformatics

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing – Ryoko Oono – PLOS One

Techniques

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions – Martin Šigut – PLOS One

** Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men – Melanie Abrahamson – Contemporary Clinical Trials Communications

Microbes on the market 

BiomX Acquires RondinX to Boost Microbiome Discovery and Development Capabilities

Vanterra Capital Backs BIOHM Health, A Total Microbiome Company

Second Genome Advances Lead, Oral Small Molecule SGM-1019, Toward Clinical Investigation in NASH After Demonstrating Safety and Tolerability in Phase 1 Study

Ed’s non-microbiology picks 

Cannabidiol (CBD) as an Adjunctive Therapy in Schizophrenia: A Multicenter Randomized Controlled Trial – Philip McGuire – The American Journal of Psychiatry

Effects of Legal Access to Cannabis on Scheduled II–V Drug Prescriptions – Sarah S. Stith – JAMDA

Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages – Enrique Peñalver – Nature Communications

Induced and controlled dietary ketosis as a regulator of obesity and metabolic syndrome pathologies – Madeline K. Gibas – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

The effect of vitamin D supplement on the score and quality of sleep in 20-50 year-old people with sleep disorders compared with control group – Mohammad Shahi Majid – Nutritional Neuroscience

Engineers create plants that glow – MIT

December 19, 2017

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Changes to the oral microbiota are associated with risk factors for oral cancer, the benefits of endophytic bacteria on plants, analysis of biofilms from a worldwide sampling of shower hoses.

Pregnancy and early life

Diversity of vaginal microbiota increases by the time of labor onset – Ekaterina Avershina – Scientific Reports

Human oral microbiome

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer – Daniela Börnigen – Scientific Reports

Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors – Jiyeon Si – Frontiers in Cellular and Infection Microbiology

Animal experiments

Pre-print: Antenatal microbial colonisation of mammalian gut – Elisa Borghi – bioRxiv

Metagenome Analysis of Bodily Microbiota in a Mouse Model of Alzheimer Disease Using Bacteria-derived Membrane Vesicles in Blood – Jin-Young Park – Experimental Neurobiology

Animal microbiome

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Plant, root, and soil microbiome

Pre-print: The ecological genetics of Pseudomonas syringae residing on the kiwifruit leaf surface – Christina Straub – bioRxiv

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Frankia diversity in host-plant root nodules is independent of abundance or relative diversity of Frankia in corresponding rhizosphere soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere – Muhammad Farhan Ul Haque – Scientific Reports

Rhizodeposition under drought is controlled by root growth rate and rhizosphere water content – Maire Holz – Plant and Soil

Water and extremophile microbiome

Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation – Wei Xie – Environmental Microbiology

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis – Ramganesh Selvarajan – MicrobiologyOpen

Distribution and phylogeny of anaerobic anammonium-oxidizing (anammox) bacteria in water column of the central Pacific Ocean – Koji Hamasaki – Deap Sea Research Part II: Topical Studies in Oceanography

Built environment

Biofilms in shower hoses – Caitlin R Proctor – Water Research

Phages and viruses

Pre-print: Human Herpes Virus 6 (HHV-6) – Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing – Colin Sharp – bioRxiv

Pre-print: ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages – Chris M Rands – bioRxiv

Bioinformatics

Pre-print: How, when, and where relic DNA biases estimates of microbial diversity – J T Lennon – bioRxiv

Metabolomics

Plasma microbiome-modulated indole- and phenyl-derived metabolites associate with advanced atherosclerosis and postoperative outcomes – Cori A Cason – Journal of Vascular Surgery

Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples – Angela K Boysen – Analytical Chemistry

Techniques

Microfluidics: A new tool for microbial single cell analyses in human microbiome studies – Yuguang Liu – Biomicrofluidics

Pre-print: CLIQ-BID: A method to quantify bacteria-induced damage to eukaryotic cells by automated live-imaging of bright nuclei – Yann Wallez – bioRxiv

Mapping the ecological networks of microbial communities – Yandong Xiao – Nature Communications

More microbes

Pre-print: Molecular insights into Vibrio cholerae’s intra-amoebal host-pathogen interactions – Charles Van der Henst – bioRxiv

Nature to the natural rescue: Silencing microbial chats – Diby Paul – Chemico-Biological Interactions

Microbes in the news

Tracking effects of a food preservative on the gut microbiome – EurekAlert

Microbiome intervention with niacin aids insulin sensitivity – Medical Xpress

Wound scanner shows bacteria glowing if your body is infected – New Scientist

Engineering new cellular scaffolding for bacteria – Celia Henry Arnaud – Chemical & Engineering News

Viruses can transfer genes across the superkingdoms of life – ScienceDaily

Microbes on the market

British Health Technology Company Expanding Into Ten European Countries – PR Newswire

December 15, 2017

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The leaders of ten research universities/institutes pledge to report student and postdoc outcomes in biomedical research as the Coalition for Next Generation Life Science initiative, commensal fungi and their cell-wall mannans can functionally replace benefits of intestinal bacteria, a new cheese starter system with improved bacteriophage resistance and antimicrobial activity.

Events and jobs

Postdoctoral Fellow, Functional Microbiome – Claesen Group, Department of Cellular and Molecular Medicine, Cleveland Clinic (also looking for interested graduate students)

Human nearly-sterile sites

Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation-related genes – Martha Scott Tomlinson – PLOS ONE

Human gut microbiome

Faecal microbiota transplantation for Clostridium difficile infection using a lyophilized inoculum from non-related donors: A case series involving 19 patients – Vigvári Szabolcs – Acta Microbiologica et Immunologica Hungarica

Animal experiments

Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria – Tony T Jiang – Cell Host & Microbe

CCL28-Deficient Mice Have Reduced IgA Antibody–Secreting Cells and an Altered Microbiota in the Colon – Kazuhiko Matsuo – The Journal of Immunology

Animal microbiome

Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid – Hiroki Dan – PLOS ONE

Plant, root, and soil microbiome

Root-derived carbon and nitrogen from beech and ash trees differentially fuel soil animal food webs of deciduous forests – Sarah L Zieger – PLOS ONE

Historical and recent land use affects ecosystem functions in subtropical grasslands in Brazil – Jan L G Leidinger – Ecosphere

Mechanisms of arsenic sequestration by Prosopis juliflora during phytostabilization of metalliferous mine tailings – Corin M Hammond

Transfer Mechanism, Uptake Kinetic Process and Bioavailability of P, Cu, Cd, Pb and Zn in Macrophyte Rhizosphere Using DGT – Shengrui Wang – Environmental Science & Technology

Food microbiology

A Multibacteriocin Cheese Starter System, Comprising Nisin and Lacticin 3147 in Lactococcus lactis, in Combination with Plantaricin from Lactobacillus plantarum – S Mills – Applied and Environmental Microbiology

Bioinformatics

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data – Marius Vital – mSystems

Discovery of carbamate degrading enzymes by functional metagenomics – Lisa Ufarté – PLOS ONE

Science, career, and publishing

A new data effort to inform career choices in biomedicine – Rebecca Blank – Science

News Feature: The science that’s never been cited – Richard Van Noorden – Nature

December 13, 2017

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Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of T. congolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider

 

December 7, 2017

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Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.

General microbiome

Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human gut microbiome

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health

Animal experiments

Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology

Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research

Water and extremophile microbiome

Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv

Phages and viruses

Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications

Bioinformatics

Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications

Techniques

In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE

More microbes

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications

Microbes in the news

Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org

What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine

Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle

Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert

Air-eating bacteria found in Antarctica – Cosmos

The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic

Microbes on the market

Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire

Precision Driven Health and Orion Health release Microbiome report – Voxy

Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal

Science, career, and publishing

How to Keep Students in Science – Howard Hughes Medical Institute

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS

Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv

Editorial: Great mentoring is key for the next generation of scientists – Nature

Amy’s non-microbiology picks

Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science

December 6, 2017

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General microbiome

Review: The Role of High-Mobility Group Box-1 and Its Crosstalk with Microbiome in Rheumatoid Arthritis – Federico Biscetti – Mediators of Inflammation

Review: The human microbiota, infectious disease, and global health: challenges and opportunities – Abraham J. Waldman – ACS Infectious Diseases

Human respiratory microbiome

The lung microbiome in patients with pneumocystosis – J. Kehrmann – BMC Pulmonary Medicine

Review: Interplay between the lung microbiome and lung cancer – Qixing Mao – Cancer Letters

 
Human skin microbiome

Effect of alcohol-based hand rub on hand microbiome and hand skin health in hospitalized adult stem cell transplant patients: a pilot study – Pranab K. Mukherjee – Journal of the American Academy of Dermatology

Human vaginal microbiome

Cervicovaginal cytokines, sialidase activity and bacterial load in reproductive-aged women with intermediate vaginal flora – Mariana Morena de VieiraSantos-Greatti – Journal of Reproductive Immunology

Human gut microbiome

The gastrointestinal behavior of saponins and its significance for their bioavailability and bioactivities – Joaquín Navarro del Hierro – Journal of Functional Foods

Anthropometric and metabolic improvements in human type 2 diabetes after introduction of an Okinawan-based Nordic diet are not associated with changes in microbial diversity or SCFA concentrations – Fang Huang – International Journal of Food Sciences and Nutrition

Systematic review: ileoanal pouch microbiota in health and disease – J. P. Segal – Alimentary Pharmacology and Therapeutics

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications – Q. Le Bastard – Alimentary Pharmacology and Therapeutics

Review: The “Gut Feeling”: Breaking Down the Role of Gut Microbiome in Multiple Sclerosis – Samantha N. Freedman – Neurotherapeutics

Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis – Mei Luo – Frontiers in Microbiology

Postoperative changes of the microbiome: are surgical complications related to the gut flora? A systematic review – Ann-Kathrin Lederer – BMC Surgery

Animal experiments

Flos Lonicera Combined with Metformin Ameliorates Hepatosteatosis and Glucose Intolerance in Association with Gut Microbiota Modulation – Na R. Shin – Frontiers in Microbiology

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Review: Nano-Se Assimilation and Action in Poultry and Other Monogastric Animals: Is Gut Microbiota an Answer? – Peter F. Surai – Nanoscale Research Letters

Interactive effects of protein and carbohydrates on production of microbial metabolites in the large intestine of growing pigs – Marcin Taciak – Archives of Animal Nutrition

Flavonoid metabolite 3-(3-hydroxyphenyl)propionic acid formed by human microflora decreases arterial blood pressure in rats – Iveta Najmanová – Molecular Nutrition & Food Research

Animal microbiome

Review: The Microbiota Regulates Immunity and Immunologic Diseases in Dogs and Cats – Ian R. Tizard – Veterinary Clinics of North America: Small Animal Practice

Exploring fish microbial communities to mitigate emerging diseases in aquaculture – Irene de Bruijn – FEMS Microbiology Ecology

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing – Yu Zuo – Plos One

Review: Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling – Elin Videvall – Molecular Ecology Resources

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality – Aura Raulo – Journal of Animal Ecology

Gene expression in the chicken caecum is dependent on microbiota composition – Jiri Volf – Veterinary Research

The response of canine faecal microbiota to increased dietary protein is influenced by body condition – Jia Xu – BMC Veterinary Research

Plant, root, and soil microbiome

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China – Keqiang Shao – Canadian Journal of Microbiology

Simultaneous adaptation and maladaptation of tree populations to local rhizosphere microbial communities at different taxonomic scales – Richard A. Lankau – New Phytologist

Water and extremophile microbiome

Phylogenetic structure and metabolic properties of microbial communities in arsenic-rich waters of geothermal origin – Simona Crognale – Frontiers in Microbiology

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake – Anikó Mentes – FEMS Microbiology Ecology

Probiotics / prebiotics

Designing synbiotics for improved human health – Sean M. Kearney – Microbial Biotechnology

Metabolomics

Blood serum metabolome of atopic dermatitis: Altered energy cycle and the markers of systemic inflammation – Aigar Ottas – Plos One

Comprehensive characterization of the in vitro and in vivo metabolites of limonin in human samples using LC-Q-TOF/MS – ShijiaLiu – Journal of Chromatography B

Anitha’s non-microbiology picks

Experiment demonstrates quantum mechanical effects from biological systems

IUCN Red List: Wild crops listed as threatened

December 5, 2017

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Today we have interesting reviews, one about proteomics and human microbiome by C.A. Kolmedar, the other about oral microbiome by L.P.Shaw and the third about human gut virome by L.A. Ogilvie. In Water section you can read the study by V.J. Koles who developed a model that simulates metagenomes and metatranscriptomes for comparison with observations. In section Bioinformatics you can read about new tools MetaLab and ASAR while in non-microbiology pics you can check podcast “Dances with rocks” with A. Denton, geologist and planetary scientist who wants to dance on Mars. Enjoy!

Jobs

Microbiology Supervisor, Rockville, Maryland

Associate Bioengineer II, Analytical R&D, Warren, NJ

Events

9th Congress of Microbiology and Parasitology Kicks Off in Cuba

General microbiome

Microbially Mediated Electrosynthesis Processes – Mohita Sharma – Microbial Fuell Cell

Development of Suitable Anode Materials for Microbial Fuel Cells – Thi Hiep Han – Microbial Fuel Cell

Progress and Future Direction of Chromosome-Centric Human Proteome Project – Young-Ki Paik – Journal of Proteome Research

Review: Proteomics and the human microbiome: where we are today and where we would like to be – Carolin Adriane Kolmeder – Emerging Topics in Life Sciences

March of the Microbes: Harnessing the Power of the Human Microbiome to Improve Health and Target Disease – Helen Albert – Clinical OMICs

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Pregnancy and early life

Development of the Microbiota in Infants and its Role in Maturation of the Gut Mucosa and the Immune System – Cecilia Ximenez – Archives of Medical Research

Human nearly-sterile sites

The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults -Xiaofeng Wen – Immunology and Microbiology

Human respiratory microbiome

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae – David W Cleary – bioRxiv

The nasopharyngeal microbiome – David W. Cleary- Emerging Topics in Life Sciences

The lung microbiome in health and disease – Miriam F Moffatt – Clinical Medicine

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report – Russell P. Bowler – Annals of the American Thoracic Society

Fungal microbiota in chronic airway inflammatory disease and emerging relationships with the host immune response – Irene Zhang – Frontiers in Microbiology

Oral microbiome

Nonleachable Imidazolium-Incorporated Composite for Disruption of Bacterial Clustering, Exopolysaccharide-Matrix Assembly, and Enhanced Biofilm Removal – Geelsu Hwang – ACS Applied Materials & Interfaces

Review: The oral microbiome – Liam P. Shaw – Emerging Topics in Life Sciences

Use of Probiotics and Oral Health – Robert P. Allaker – Current Oral Health Reports

Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing – Jeffrey B. Payne – mSphere

Human vaginal microbiome

The human female urogenital microbiome: complexity in normality – David A. MacIntyre – Emerging Topics in Life Sciences

Human gut microbiome

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

The gut microbiome and hypertension – Pevsner-Fischer – Current Opinion in Nephrology and Hypertension

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota – Ibrahim Hamad – Scientific Reports

Lymphatic system and gut microbiota affect immunopathology of neuroinflammatory diseases, including multiple sclerosis, neuromyelitis optica and Alzheimer’s disease – Ikuo Tsunoda – Clinical & Experimental Neuroimmunology

Effect of different treatments and alcohol addiction on gut microbiota in minimal hepatic encephalopathy patients – Zan Zuo – Experimental and Therapeutic Medicine

Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease – Paula Perez-Pardo – Current Behavioral Neuroscience Reports

Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions – Jingao Yu – Journal of Ethnopharmacology

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Gut microbiota in human SLE and a mouse model of lupus – Xin M. Luo – Applied and Environmental Microbiology

The interaction between smoking, alcohol and the gut microbiome – Gabriele Capurso – Best Practice & Research Clinical Gastroenterology

Animal experiments

Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids’ metabolomics relationships in dairy cows – Hui-Zeng Sun – BMC Genomics

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – Junhyung Kim – Gut Pathogens

Chronic glucocorticoid treatment induced circadian clock disorder leads to lipid metabolism and gut microbiota alterations in rats – Tao Wu – Life Sciences

Animal microbiome

Gut microbiota composition is associated with environmental landscape in honey bees – Julia C Jones –  Ecology and Evolution

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams – M. Milan – Aquatic Toxicology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – Jin-JaeLee  – Food Research International

Plant, root, and soil microbiome

Studies on mycorrhizal biodiversity in medicinal plant species of Pookode lake area, Wayanad, Kerala, India – Saranya Babu Jayaprakash C.M. – Annals of Plant Sciences

Effects of Iron Amendments on the Speciation of Arsenic in the Rice Rhizosphere after Drainage – Noriko Yamaguchi – Soils

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora – Hongjun Liu – Plant and Soil

Seasonal changes in a maize-based polyculture of central Mexico reshape the co-occurrence networks of soil bacterial communities – Eria A. Rebollar – Frontiers in Microbiology

Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil – Hongna Li – Ecotoxicology and Environmental Safety

Roles of different active metal-reducing bacteria in arsenic release from arsenic-contaminated paddy soil amended with biochar – Jiang-taoQiao – Journal of Hazardous Materials

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil – Chanyarat Paungfoo-Lonhienne – Scientific Reports

Responses of soil nutrients and microbial communities to three restoration strategies in a karst area, southwest China – Dejun Li – Journal of Environmental Management

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils – Robert Wagner – Environmental Microbiology

Water and extremophile microbiome

Ocean biogeochemistry modeled with emergent trait-based genomics – V. J. Coles – Science

Bacterial Community Profiling of Waters from Aquaculture and Non-aquaculture Sites within Taal Lake Ecosystem through 16S rDNA Analysis – Leslie Michelle M. Dalmacio – The Philippine Journal of Health Research and Development

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments as Revealed by 454 Pyrosequencing – Yin-Xin Zeng –  Frontiers in Microbiology

Microbial communities shaped by treatment processes in a drinking water treatment plant and their contribution and threat to drinking water safety – Qi Li – Frontiers in Microbiology

Diversity of microbial communities and quantitative chemodiversity in layers of marine sediment cores from an causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers in Microbiology

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids – Caroline S. Fortunato –  Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment and water bacterial communities – Arthur Escalas – Environmental Microbiology

Built environment

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm – Pampillón-González L – Journal of Molecular Microbiology and Biotechnology

Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim – Dong Wu – Applied Microbiology and Biotechnology

Effect of ammonia on the active microbiome and metagenome and from stable full-scale digesters – J.Ruiz-Sánchez – Bioresource Technology

Droplet distribution and airborne bacteria in an experimental shower unit – C.E.Estrada-Perez – Water Research

Food Microbiology

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation – Xueshan Wang – Applied and Environmental Microbiology

Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages -Ilario Ferrocino –  Applied and Environmental Microbiology

Probiotics / prebiotics

Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers – A P Allen  – Translational Psychiatry

Phage and viruses

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study – Hideo Shigeishi – Biomedical Reports

Kullback Leibler divergence in complete bacterial and phage genomes – Sajia Akhter – PeerJ

Review: The human gut virome: form and function – Lesley A. Ogilvie – Emerging Topics in Life Sciences

Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu – Mao-KeLiu – Food Research International

Bioinformatics

Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads – Fanny Perraudeau – bioRxiv

MetaLab: an automated pipeline for metaproteomic data analysis – Kai Cheng – Microbiome

ASAR: visual analysis of metagenomes in R – Askarbek Orakov – Bioinformatics

Bacteria & Biofuels

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol – Liang Tian – Biotechnology for Biofuels

Biophotovoltaics: Conversion of Light Energy to Bioelectricity Through Photosynthetic Microbial Fuel Cell Technology – Rashmi Chandra – Microbial Fuel Cell

Techniques

Electron microscopy reveals unique nano forms of bacterial spores – Sumanta Ghosh – bioRxiv

Continuous and High-throughput Electromechanical Lysis of Bacterial Pathogens using Ion Concentration Polarization – Minseok Kim – Analytical Chemistry

Microbes in the news

A New Antibiotic Weakness—Drugs Themselves Help Bacteria Survive

Exercise Changes Gut Microbial Composition Independent of Diet, Study Shows

Bacteria and obesity: Reviewing the connection between gut bacteria, obesity, and diet

Bacteria & Art

Bacteria Collection of Icons Vector Illustration

Tina’s non microbiology picks

PODCAST: This Scientist Wants To Dance On Mars (And She Just Might Make That Happen)

How to Review a Manuscript

December 4, 2017

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Today we have many interesting articles,  Marangoni A. evaluates  antifungal properties of Spirulina platensis against  Candida species; J. de Gunzburg  reports on gut microbiome  protection from antibiotics; E. Uhlig writes about removal of Escherichia coli from “ready‐to‐eat” salads .. while in my personal non microbiological pics you can read the study from A.Carter about women’s visibility in academic seminars. Apparently women ask fewer questions than men. Enjoy your winter read.

Events and jobs

Microbiology Professor, College of the Sequoias, San Jose

Postdoctoral Fellow, EMBL,Hinxton, United Kingdom

General microbiome

Review: Multidrug resistant (or antimicrobial-resistant) pathogens – alternatives to new antibiotics? – Anne-Sophie Brunel – Swiss Medical Weekly

Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s – Grote M – History and Philosophy of the Life Sciences

Pregnancy and early life

32-week premature rupture of membranes caused by oropharyngeal microbiota – Alberto Hidalgo-Chicharro – Microbiology Society

Bacteriological and Immunological Profiling of Meconium and Fecal Samples from Preterm Infants: A Two-Year Follow-Up Study – Marta Gómez – Nutrients

Human respiratory microbiome

IL-17 and TNF-α Are Key Mediators of Moraxella catarrhalis Triggered Exacerbation of Allergic Airway Inflammation – Safa Alnahas – Frontiers in Immunology

Oral microbiome

Gingivitis and plaque prevention using three commercially available dentifrices: A comparative clinical and microbiological randomized control parallel study – Ramprasad Reddy – International Journal of Pharmaceutical Investigation

Human vaginal microbiome

In vitro activity of Spirulina platensis water extract against different Candida species isolated from vulvo-vaginal candidiasis cases – Antonella Marangoni – PLOS One

Characterization of a New Ezakiella Isolated From the Human Vagina: Genome Sequence and Description of Ezakiella Massiliensis Sp. Nov – K Diop – Current Microbiology

Newly Isolated Lactobacilli Strains From Algerian Human Vaginal Microbiota: Lactobacillus Fermentum Strains Relevant Probiotic’s Candidates – Liza Ouarabi – Probiotics and Antimicrobial Proteins

Human nearly-sterile sites

A comprehensive analysis of breast cancer microbiota and host gene expression – Kevin J. Thompson – PLOS One

Human gut microbiome

Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut–Muscle Axis? – Andrea Ticinesi – Nutrients

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Benedicte F. Jordan – Current Pathobiology Reports

Protection of the human gut microbiome from antibiotics – Jean de Gunzburg – The Journal of Infectious Diseases

Gut microbiota and colorectal cancer: insights into pathogenesis for novel therapeutic strategies – Yongbo Kang – Zeitschrift für Gastroenterologie

Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample – Joon Yong Kim – Frontiers in Pharmacology

Cellular senescence in gastrointestinal diseases: from pathogenesis to therapeutics – Frey N – Nature Reviews Gastroenterology

Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism – Chatzidaki-Livanis M – mBio

Reduction in Gut Microbial Diversity as a Mechanism of Action of Exclusive Enteral Nutrition – Kaakoush NO – The American Journal of Gastroenterology

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Jordan BF – Current Pathobiology Reports

Review: A review of metabolic potential of human gut microbiome in human nutrition – Yadav M – Archives of Microbiology

Animal experiments 

Colonization with Escherichia coli EC 25 protects neonatal rats from necrotizing enterocolitis – Debi M. Thomas – PLOS One

Animal microbiome

Bamboo Specialists From Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbe – EA McKenney – Microbial Ecology

Plant, root, and soil microbiome

Organic Amendments in a Long-Term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis – CAO Schmid – Microbial Ecology

Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest – D Kerfahi – Microbial Ecology

Water and extremophile microbiome 

Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China – Hongpeng Cui – Current Microbiology

Built environment

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge – Jing Wu – International Journal of Environmental Research and Public Health

Food microbiology

Effects of household washing on bacterial load and removal of Escherichia coli from lettuce and “ready-to-eat” salads – Elisabeth Uhlig – Food Science & Nutrition

Organic food and the impact on human health – Hurtado-Barroso S – Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Probiotics Ingestion Does Not Directly Affect Thyroid Hormonal Parameters in Hypothyroid Patients on Levothyroxine Treatment – Giorgia Spaggiari – Frontiers in Endocronology

Characterization of probiotic potential of Bacillus species isolated from a traditional brine pickle – Ragul K – Journal of Food Science and Technology

 

Bioinformatics

Microbiome Datasets Are Compositional: And This Is Not Optional – Gregory B. Gloor – Frontiers in Microbiology

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community – Herschend J – Scientific Reports

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform – Monica Pichler – bioRxiv

Techniques

Exploration of Microbial Communities Using the Thermo Scientific Varioskan LUX Multimode Reader and the Invitrogen EVOS FL Cell Imaging System – Anna Hiltunen – BioTechniques

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria – Giantommaso Scarascia – BMC Microbiology

Microbes in the news

Microorganisms on your scalp, ears and elbows can be turned into music

Microbes on the market

With $1M in funding, Phase Genomics looks to crack genetic codes and discover unknown bacteria

Tina’s non microbiological pics

Women’s visibility in academic seminars: women ask fewer questions than men

 

December 1, 2017

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Happy December! Today’s digest features research articles on prion like domains in phages, effect of high salt challenge on gut microbiota and immune system. Enjoy!

Events and jobs

Assistant Professor, Statistics and Microbiology – The University of Manitoba

Program Manager, Microbiology – RWJ-Pathology-PISC

General microbiome

Review: Experimental design and quantitative analysis of microbial community multiomics – Himel Mallick – Genome Biology

Pregnancy and early life

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants – Priscila T. Dobbler – Frontiers in Microbiology

Human respiratory microbiome

Colonic Bacteroides are positively associated with trabecular bone structure and programmed by maternal vitamin D in male but not female offspring in an obesogenic environment – C R Villa – International Journal of Obesity

Human skin microbiome

Diversity of bacterial communities on the facial skin of different age-group Thai males – Alisa Wilantho – PeerJ

Human oral microbiome

Oral Health and the Oral Microbiome in Pancreatic Cancer: An Overview of Epidemiological Studies – Paige M Bracci – The Cancer Journal

Bacterial alterations in salivary microbiota and their association in oral cancer – Wei-Hsiang Lee – Scientific Reports

Human vaginal microbiome

Review : Is bacterial vaginosis a disease? – Gregor Reid – Applied Microbiology and Biotechnology

Human gut microbiome

The gut mycobiome of the Human Microbiome Project healthy cohort – Andrea K. Nash – Microbiome

Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment – Yanyun Gu – Nature Communications

*Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice – Sean R.Llewellyn – Gastroenterology

Psychobiotics: A new approach for treating mental illness? – Snigdha Misra – Critical Reviews in Food Science and Nutrition

Small Intestinal Bacterial Overgrowth: Should Screening Be Included in the Pre-fecal Microbiota Transplantation Evaluation? – Jessica R. Allegretti – Digestive Diseases and Sciences

Gut microbiota-mediated generation of saturated fatty acids elicits inflammation in the liver in murine high-fat diet-induced steatohepatitis – Shoji Yamada – BMC Gastroenterology

Animal experiments

Vertical vs. horizontal transmission of the microbiome in akey disease vector, Ixodes pacificus – Jessica Y. Kwan – Molecular Ecology

Gut Microbiome-induced Shift of Acetate to Butyrate Positively Manages Dysbiosis in High Fat Diet – Xu Si – Molecular Nutrition and Food Research

Increased cortical neuronal responses to NMDA and improved attentional set-shifting performance in rats following prebiotic (B-GOS®) ingestion – Benjamin Gronier – European Neuropsychopharmacology

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens – Zhui Li – Plos One

Doxycycline induces dysbiosis in female C57BL/6NCrl mice – Felicia D. Duke Boynton – BMC Research Notes

Animal microbiome

The effect of dietary energy and protein levels on body weight, size, and microflora of ostrich chicks – Tahereh Nikravesh-Masouleh – Tropical Animal Health and Production

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion – Miriam E. Shiffman – PeerJ

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs – Ana Carolina M. Junqueira – Scientific Reports

Plant, root, and soil microbiome

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China – Jianming Wang – Frontiers in Microbiology

Water and extremophile microbiome

Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model – Wei Li – Molecular Ecology

Microbial Reduction of Fe(III) and SO42− and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments – Ji-Hoon Lee – Microbial Ecology

The influence of complex fermentation broth on denitrification of saline sewage in constructed wetlands by heterotrophic nitrifying/aerobic denitrifying bacterial communities – Guiping Fu – Bioresource Technology

Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats – Marcelo Baeza – Frontiers in Microbiology

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh – Edwin T. Gnanaprakasam – mBio

Probiotics / prebiotics

Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf? – T.T.Yohe – Journal of Dairy Science

Review: Effect of Probiotic Supplementation on CD4 Cell Count in HIV-Infected Patients: A Systematic Review and Meta-analysis – Asma Kazemi – Journal of Dietary Supplements

Phages and viruses

*Prion-Like Domains in Phagobiota – George Tetz – Frontiers in Microbiology

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior – Elaine Luo – mBio

Anitha’s non-microbiology picks

Hubble in a bubble: Scallop eyes act just like tiny telescopes

Jackpot of fossilized pterosaur eggs unearthed in China

Sorry, Grumpy Cat: Study finds dogs are brainier than cats