Category Archives: Bik’s Non-Microbiology Picks

January 24, 2018

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General microbiome

Meta-analysis generates and prioritizes hypotheses for translational microbiome research – Claire Duvallet – microbial biotechnology

Resistance to Antibiotics: Are we prepared to Handle This Growing Ghost? – Ashima Kushwaha Bhardwaj – Omics Ebook Group

Pregnancy and early life

Neonate gut and respiratory microbiota: coordinated development through time and space – Alex Grier – bioRxiv

Human oral microbiome

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications – A. Mira – Advances in Dental Research (SAGE Journals)

Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols – L. Zhan – Advances in Dental Research (SAGE Journals)

The Caries Microbiome: Implications for Reversing Dysbiosis – A.C.R. Tanner – Advances in Dental Research (SAGE Journals)

In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P. D. Marsh – Advances in Dental Research (SAGE Journals)

Getting to Know “The Known Unknowns”: Heterogeneity in the Oral Microbiome – R. A. Burne – Advances in Dental Research (SAGE Journals)

Human gut microbiome

Adaptive Immune Education by Gut Microbiota Antigens – Qing Zhao – Immunology

Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Characterization of the fecal microbiota differs between age groups in Koreans – Sun-Young Kook – Intestinal Research

Diet, microbiota and inflammatory bowel disease: review – Bruna Luísa Radavelli – Nutrition & Food Science

The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori – Ingeborg Klymiuk – Frontiers in Microbiology

Gut Microbial Diversity in Women with Polycystic Ovary Syndrome Correlates with Hyperandrogenism – Pedro J Torres – JCEM

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls – Sudarshan A Shetty – bioRxiv

Animal experiments 

Modeling Host-Microbiome Interactions in Caenorhabditis elegans – Teklu K. Gerbaba – Journal of Nematology

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota – Zoya Alteber – Immunology & Cell Biology

A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols – Mei Cheng – Food & Function

Animal microbiome

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica – Juan G. Abarca – Frontiers in Microbiology

Functional Characteristics of the Flying Squirrel’s Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling – Hsiao-Pei Lu – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation – József Geml – New Phytologist

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

Assembly and ecological function of the root microbiome across angiosperm plant species – Connor R. Fitzpatrick – PNAS

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome – Jaderson Silveira Leite Armanhi – Frontiers in Plant Science

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function – Baneshwar Singh – Frontiers in Microbiology

Water and extremophile microbiome

Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O Roger Anderson – Frontier in Marine Science

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields – Teresa Cerqueira – Environmental Microbiology

Bioinformatics

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems – Ángel Martín Ortiz-Estrada – Reviews in Agriculture

[MSc Thesis] Optimizing the Reconstruction of Microbial Population Genomes from Metagenomes – Bhavya Nalagampalli Papudeshi – San Diego State University, ProQuest Dissertations Publishing

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Extension of the viral ecology in humans using viral profile hidden Markov models – Zurab Bzhalava – PLOS One

Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection – Karthika Suryaletha – International Wound Journal

A strategy for association study on intestinal microbiome and brain metabolome across lifespan of rats – Tianlu Chen – Analytical Chemistry

Techniques

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows – Jueeli D. Vaidya – Frontiers in Microbiology

Microbes in the news

Hyperandrogenism may alter gut microbiome in PCOS

Ed’s non-microbiology picks 

Using Fungi to Fix Bridges

Cooperating with machines – Jacob W. Crandall – Nature Communications

An investigation into the nutritional composition and cost of gluten-free versus regular food products in the UK – L. Fry – Journal of Human Nutrition and Dietetics

Prevalence and Trends in Prepregnancy Normal Weight — 48 States, New York City, and District of Columbia, 2011–2015 – CDC / Morbidity and Mortality Weekly Report

Exposed subsurface ice sheets in the Martian mid-latitudes – Colin M. Dundas – Science

Shorter sleep duration and longer sleep onset latency are related to difficulty disengaging attention from negative emotional images in individuals with elevated transdiagnostic repetitive negative thinking – Jacob A. Nota – Journal of Behavior Therapy and Experimental Psychiatry

January 19, 2018

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Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

January 13, 2018

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100+ alerts, meaning great papers in every category. Enjoy!

General microbiome
Review: Sphingolipids in host-microbial interactions – Stacey L Heaver – Current Opinion In Microbiology

Editorial: The Human Microbiome – Emily P Balskus – ACS Infectious Diseases

Review: Emergent Heterogeneous Micro-environments in Biofilms:Substratum Surface Heterogeneity and Bacterial Adhesion Force-sensing – Yijin Ren – Fems Microbiology Reviews

Pregnancy and early life
Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses – Thomas H A Ederveen – Microbiome

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study – Anne K Örtqvist – Gut

Review: Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited – Michael J Nash – Frontiers In Endocrinology

Human respiratory microbiome
Genomics of Corynebacterium striatum, an emerging multi-drug resistant pathogen of immunocompromised patients – Kathleen Nudel – Clinical Microbiology And Infection

Human skin microbiome
Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression – Grith M M Hermansen – Fems Microbiology Letters

Human oral microbiome
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer – Richard B Hayes – JAMA Oncology

Composition of salivary microbiota in elderly subjects – Taiji Ogawa – Scientific Reports

Human gut microbiome
CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi – Irina Leonardi – Science (New York, N.Y.)

Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. – Wenjing Zhao – Science (New York, N.Y.)

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients – Bryan T. Nycz – PLoS One

Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures – Regina Lamendella – mSphere

Alterations of the gut microbiota in Hashimoto’s thyroiditis patients – Fuya Zhao – Thyroid : Official Journal Of The American Thyroid Association

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2 – Ahmad Ali-Ahmad – Journal Of Structural Biology

Review: Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases – Xuan Li – Frontiers In Immunology

Review: Pathogens, microbiome and the host: emergence of the ecological Koch’s postulates – Pascale Vonaesch – FEMS Microbiology Reviews

Review: Biochemistry of Complex Glycan Depolymerisation by the Human Gut Microbiota – Didier Ndeh – FEMS Microbiology Reviews

Review: Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world – Pamela Schnupf – Current Opinion In Microbiology

Microbial Ecology
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information – Ignace L M M Tack – Frontiers In Microbiology

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems – Elham Ehsani – Scientific Reports

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors – Holger Brüggemann – Scientific Reports

Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s – Alita R. Burmeister – The American Naturalist

Animal experiments
Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice – Kristin L Connor – Biology of Reproduction

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment – Ira Ekmekciu – Frontiers In Microbiology

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota – Richard Van Vleck Pereira – Scientific Reports

Gama-aminobutyric Acid Enriched Rice Bran Diet Attenuates Insulin Resistance and Balances Energy Expenditure via Modification of Gut Microbiota and SCFAs – Xu Si – Journal Of Agricultural And Food Chemistry

Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria – Eiichiro Yasutomi – Digestive Diseases And Sciences

Rhubarb supplementation promotes intestinal mucosal innate immune homeostasis through modulating intestinal epithelial microbiota in goat kids – Jinzhen Jiao – Journal Of Agricultural And Food Chemistry

Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats – N Marungruang – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Exercise Prevents Enhanced Postoperative Neuroinflammation and Cognitive Decline and Rectifies the Gut Microbiome in a Rat Model of Metabolic Syndrome – Xiaomei Feng – Frontiers In Immunology

Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota – Tania Rosas – Fems Microbiology Ecology

Gut Flora-Dependent Metabolite Trimethylamine-N-oxide Accelerates Endothelial Cell Senescence and Vascular Aging through Oxidative Stress – Yilang Ke – Free Radical Biology & Medicine

Nanocomposite of Half-Fin Anchovy Hydrolysates/Zinc Oxide Nanoparticles Exhibits Actual Non-Toxicity and Regulates Intestinal Microbiota, Short-Chain Fatty Acids Production and Oxidative Status in Mice – Ru Song – Marine Drugs

Animal microbiome
Is there a link between aging and microbiome diversity in exceptional mammalian longevity? – Graham M. Hughes – PeerJ (Specifically, bats or Myotis myotis)

Gut Microbes Egested during Bites of Infected Sand Flies Augment Severity of Leishmaniasis via Inflammasome-Derived IL-1β – Ranadhir Dey – Cell Host & Microbe

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera – Maryam Chaib De Mares – Frontiers In Microbiology (from December 2017)

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. – Mabel T Wong – Frontiers In Microbiology (from December 2017)

Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities – Oliver Otti – Frontiers In Immunology

Plant, root, and soil microbiome
Forest conversion induces seasonal variation in microbial β-diversity – Shengen Liu – Environmental Microbiology

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils – Peng Liu – Chemosphere

Intra-species variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes – Cui-Jing Zhang – Environmental Microbiology Reports

Positive diversity-functioning relationships in model communities of methanotrophic bacteria – Elvira Schnyder – Ecology

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field – Bryan D. Emmett – Frontiers in Microbiology (from December 2017)

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages – Miao Yang – Plos One

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – Environmental Microbiology Reports

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient – Bonnie Waring – FEMS Microbiology Ecology

Review: Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils – Ruth Gómez Expósito – Frontiers in Microbiology (from December 2017)

Water and extremophile microbiome
Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective – J. Sánchez-España – GeoBiology

Responses of Periphyton to Fe2O3 Nanoparticles: A Physiological and Ecological Basis for Defending Nanotoxicity – Jun Tang – Environmental Science & Technology

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores – Binu Mani Tripathi – Scientific Reports

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic – Patryk Krauze – Frontiers In Microbiology

In Situ Field Sequencing and Life Detection in Remote (79°26’N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities – J Goordial – Frontiers In Microbiology (from December 2017)

Built environment
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers In Microbiology

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities – Irina Gudakova – The Pediatric Infectious Disease Journal

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge – Ajoy Roy – Bioresource Technology

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater – Gyuseong Han – Environmental Science And Pollution Research International

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation – Martin Sperfeld – Water Research

Review: Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances – Lili Miao – Science China. Life Sciences

Food microbiology
Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System – Shima Sadeghi Ekbatan – Foods (Basel, Switzerland)

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice – Chao Tang – Food & Function

A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract – Eva-Maria Pferschy-Wenzig – Frontiers In Pharmacology

Review: Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview – Sandra Maria Barbalho – Journal Of Medicinal Food

Probiotics / prebiotics / antibiotics
The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms – Anna de Breij – Science Translational Medicine

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure – Daisuke Sasaki – Scientific Reports

Single Cell Observations Show Persister Cells Wake Based on Ribosome Content – Jun-Seob Kim – bioRxiv

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis. – Mark Lyte – Plos One

Phages and viruses
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. – Evans Atoni – Viruses

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments – Verona Vandieken – Frontiers In Microbiology

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis – Soner Yildiz – Microbiome

Genome Announcements
Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota. – Mossaab Maaloum – Genome Announcements

Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome. – Aline C Freitas – Genome Announcements

‘Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother – A H Togo – New Microbes And New Infections

Microbes in the news
AGA enrolls 1st patient into largest planned fecal microbiota transplantation study – Eric Oliver – GI & Endoscopy

Will This Swallowable Sensor Replace Colonoscopies? – Bob Curley – HealthLine

**A Patient’s Journey: Taming the Glucose Monster – Howard Wolinsky – MedPage Today**

Microbes on the market
CoreBiome Bolsters Its Board of Directors with the Addition of Daniel Pomp, Ph.D. – BusinessWire

Curetis and MGI Advance Strategic Partnership in NGS-Based Molecular Microbiology – BioSpace

Science, publishing, and career
“Available upon request”: not good enough for microbiome data! – Morgan G I Langille – Microbiome

Tiffany’s non-microbiology picks
Chemists go green to make better blue jeans – Nature
I did not know demin was so dirty until I heard about Everlane’ new jeans – and now there are new method to make them!

January 7, 2018

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Today’s digest is brief but full of fun and exciting news about microbes, including self-portraits of microbes on your skin and how AI (artificial intellegence) is used to identify bacteria.

Gut Microbiome

REVIEW: Gut as a target for cadmium toxicity. Tinkov, AA. Environmental Pollution

Plant, Soil, and Water Microbiome

Effects of short-term fallow managements on soil microbial properties: A case study in China. Li, G. Applied Soil Ecology

Animal Experiments and Microbiome

Environmental concentrations of antibiotics impair zebrafish gut health. Zhou, L. Environmental Pollution

Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish. Jin, Y. Environmental Pollution

Food Microbiome

REVIEW: Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging. Odeyemi, OA. International Journal of Food Microbiology.

Microbes in the NEWS

The Swab Test: Amount Of Bacteria On Touchscreens May Surprise You

-CBS Philly

Artificial intelligence used to identify bacteria

-Digital Journal

Physicists Solve the Biodiversity Arms-Race Paradox: “Kill the Winner”

-Inverse

A Self-Portrait of the Microbes that Live on our Skin

-Labiotech.eu (blog)

Microbiology Jobs

Part-Time Lab Technician II, Biology/Microbiology

-Inside Higher Ed Careers

January 3, 2018

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Today we have a nice event /training in social science techniques organized by NERC in Manchester, Bristol and Edinburgh (UK), few microbiology jobs, an interesting review from Arun T. Nair in “Gut Microbiome”, quite a few papers about Synechococcus in “Water and extremophile microbiome”. Check as well “Microbes on market” where you can read about Google and Microsoft investing in medicine startup DNAnexus.

Events

Social science techniques for natural scientists training funded by NERC, UK

Jobs

Microbiologist – Kent, UK

Scientist/Sr.Scientist – Strain Development, CJM Talent Solutions, San Francisco, US

Associate/Assistant Professor : Miami, Florida, FL, US

General microbiome

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds – Clifford G. Clark – PLOS

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing – Heather P. McLaughlin -PLOS

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis – Anita Loeschcke -PLOS

Pregnancy and early life

Effect of innate antiviral glycoproteins in breast milk on seroconversion to rotavirus vaccine (Rotarix) in children in Lusaka, Zambia – Katayi Mwila-Kazimbaya – PLOS

Oral microbiome

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis – Isabela N. Rôças – PLOS

Human vaginal microbiome

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study – Erica L. Plummer – PLOS

Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14 – Traci Ness – PLOS

Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis – Jennifer K. Lee – Nature Communications

Human gut microbiome

T6SS: The bacterial “fight club” in the host gut – Thibault G. Sana – PLOS Pathogens

Review: Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson’s Disease: A Critical Review – Arun T Nair – Journal of Neurogastroenterology and Motility

Animal experiments

Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens – X M Ding – Poultry Science

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS

Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility – Angela M. Henschel – PLOS

Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens  – C Forte – Poultry Science

Animal microbiome

Oral Disease and Microbiota in Free-Roaming Cats – Ana Whyte – Topics in Companion Animal Medicine

Review: Effect of Enterococcus Faecium Strain SF68 on Gastrointestinal Signs and Fecal Microbiome in Cats Administered Amoxicillin-Clavulanate – C. Torres-Henderson – Topics in Companion Animal Medicine

Water and extremophile microbiome

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea – Francesca De Martini – Limnology and Oceanography

Microbial proteins for organic material degradation in the deep ocean – David L. Kirchman – PNAS

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons – Yihwan Kim – PLOS

Potential impact of global climate change on benthic deep-sea microbes – Roberto Danovaro – FEMS Microbiology Letters

Variability in the production of organic ligands, by Synechococcus PCC 7002, under different iron scenarios – Guillermo Samperio-Ramos – Journal of Oceanography

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study – Yangyang Lu – Biogeosciences

Microbial diversity of saline environments: searching for cytotoxic activities – Carolina Díaz-Cárdenas – AMB Express

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses – Deepak Kumaresan – BMC Microbiome

Probiotics / prebiotics

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Modifying progression of aging and reducing the risk of neurodegenerative diseases by probiotics and synbiotics – Huey Shi Lye – Frontiers In Bioscience

Phages and viruses

Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves – Pantelis Katharios – PLOS

High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns – Zizipho Z. A. Mbulawa – PLOS

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis – Luis E. M. Villegas – PLOS

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins – David Baltrus – bioRxiv

Bioinformatics

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing – Chao Fang – Giga Science

 

Techniques

Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography – João M Medeiros – Current Opinion in Microbiology

Microbes in the news

Tech company’s lights being used to kill germs in ambulances

Astronauts Identify Mystery Microbes in Space for the 1st Time

Microbes on the market

Seres Therapeutics Inc (MCRB) Holdings Increased by State Street Corp

Microsoft, Google invest in precision medicine startup DNAnexus

Tina’s non-microbiology picks

Synthetic Biology in the Driving Seat of the Bioeconomy – Yensi Flores Bueso – Trends in Biotechnology

Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

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 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