Category Archives: Human reproductive or urinary

February 12, 2018

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A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.

Events

Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease

Metabolomics

Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science

Technology

Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune

 

February 8, 2018

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Many interesting articles today: the geographical location of habitat has a stronger impact on the fecal microbiome of lemurs than sex, age, or species;  the mechanism for pathobiont-dependent inflammatory bowel disease involves microbiota reactive T cells; highly active antiretroviral therapy can restore gut microbiome diversity in AIDS patients; host immunity can interact with skin microbiota composition as shown in two species of giant salamander; the development of the small intestine microbiome in silka deer; and the gut microbiome of preterm infants that are breastfed develops normally.

Events and jobs

FEMS Project: Volunteer for the Opportunities Board Taskforce

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General microbiome

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists – A. B. F. Ivens – Molecular Ecology

Pregnancy and early life

Maternal antibiotic exposure during pregnancy and hospitalization with infection in offspring: a population-based cohort study – Jessica Eden Miller – International Journal of Epidemiology

*Intestinal microbiota development and gestational age in preterm neonates – Katri Korpela – Scientific Reports

Human oral microbiome

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population – Gao, Xiaowei MM – Medicine

Human vaginal microbiome

Commentary: The implausible “in vivo” role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota – Gilda Tachedjian – Microbiome

Human gut microbiome

Microbiome–host systems interactions: Protective effects of propionate upon the blood–brain barrier – Lesley Hoyles – bioRxiv

*Alterations in the gut microbiota of patients with acquired immune deficiency syndrome – Youlian Zhou – Journal of Cellular and Molecular Medicine

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons – Amy Wallis – Microbiome

Review: Diet and microbiota linked in health and disease  – T. Requena – Food And Function

Review: The role of gut microbiota and IL-23/IL-17 pathway in ankylosing spondylitis immunopathogenesis: New insights and updates – Farhad Babaie – Immunology Letters

Dissertation: Interaction of Cocoa Powder with Intestinal Microbiota – Zuyin Li – Louisiana State University


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Animal experiments

*c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont – Mo Xu – Nature

Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity – Prasant Kumar Jena – The FASEB Journal

High-fat diet stimulates the gut pathogenic microbiota and maintains hepatic injury in antibiotic-treated rats – Sooad Al-Daihan – Cellular and Molecular Biology

Review: Searching for the gut microbial contributing factors to social behavior in rodent models – Brittany D. Needham – Developmental Neurobiology

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria – Evelyne Mann – Frontiers in Microbiology


Animal microbiome

*Occupancy strongly influences faecal microbial composition of wild lemurs – Alexander Umanets – FEMS Microbiology Ecology

*Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders – Obed Hernández-Gómez – Molecular Ecology

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities – Christine P. Zolnik – Tick and Tick-borne Diseases

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning – Zhipeng Li – Frontiers in Microbiology

Exploring coral microbiome assemblages in the South China Sea – Lin Cai – Scientific Reports

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea – Esther Rubio-Portillo – Frontiers in Microbiology

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties – Elodie Denet – PLOSone

Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.) – Xiaofeng Xia – Frontiers in Microbiology

Effects of predation stress and food ration on perch gut microbiota – Yinghua Zha – Microbiome

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability – Jason A. Rothman – Microbial Ecology


Plant, root, and soil microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain – Yu Shi – Microbiome

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities – Li Zhaolei – Ecotoxicology and Environmental Safety

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils – Mira Mutschlechner – FEMS Microbiology Ecology

Diversity and metabolic potential of the microbiota associated with a soil arthropod – Simon Bahrndorff – Scientific Reports

Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China – Jia Liu – Journal of Soils and Sediments

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate – Larisa Cortes-Tolalpa – Applied Microbiology and Biotechnology

Commentary: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Review: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? – Christina Hazard – New Phytologist

Review: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection


Water and extremophile microbiome

Ultra-rare marine microbes contribute to key sulfur related ecosystem functions – Dimitri Kalenitchenko – Molecular Ecology

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea – Keon Hee Kim – Applied Biological Chemistry

Built environment

Airborne microbial communities in the atmospheric environment of urban hospitals in China – Xin-Lei Gao – Journal of Hazardous Materials


Food microbiology

Effects of chitosan oligosaccharides on microbiota composition of silver carp (Hypophthalmichthys molitrix) determined by culture-dependent and independent methods during chilled storage – Shiliang Jia – International Journal of Food Microbiology

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Probiotics / prebiotics

Lactobacillus plantarum AN1 cells increase caecal L. reuteri in an ICR mouse model of dextran sodium sulphate-induced inflammatory bowel disease – Yasushi Yokota – International Immunopharmacology

Lactobacillus salivarius LA307 and Lactobacillus rhamnosus LA305 attenuate skin inflammation in mice – S. Holowacz – Beneficial Microbes

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions – M. Ray – Beneficial Microbes

Lactobacillus rhamnosus GG Affects Microbiota and Suppresses Autophagy in the Intestines of Pigs Challenged with Salmonella Infantis – Wei Zhang – Frontiers in Microbiology

Probiotic Use in Equine Gastrointestinal Disease – Angelika Schoster – Veterinary Clinics: Equine Practice

Review: The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Journal of the Science of Food and Agriculture

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits – Agnieszka Mika – Neuroscience Letters

Biotechnology

Effects of voltage on sulfadiazine degradation and the response of sul genes and microbial communities in biofilm-electrode reactors – Xiao-Li Yang – Ecotoxicology and Environmental Safety

Waste and Pollution

Biodegradation of n-alkanes on oil–seawater interfaces at different temperatures and microbial communities associated with the degradation – Synnøve Lofthus – Biodegradation

Techniques

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens – Stefanie U. Wetzels – PLOSone

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? – Ylva Lekberg – New Phytologist


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Microbes in the news

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets – Signe Dean – Science Alert

The discovery of a third form of flagella-mediated motility in symbiotic bacteria – Phys.org

Phage or foe? – In light of new evidence, we have to reassess the role of bacteriophages in microbial communities: are they always the enemy? – Lucía Fernández – npj Biofilms and Microbiomes

The effect of gut bacteria on bone health cannot be generalized – Randi Lundberg – Taconic

Here’s What You Need To Know About The Bacteria In Your Vagina
A microbiome doesn’t just exist in your gut – Sarah DiGiulio – Huffington Post

Understanding Microbial Communities Living On Amphibian Skin – Sofia Prado-Irwin – Science Trends

In the battle against cancer, microbes could be the answer – Nicola Davison – Wired


February 7, 2018

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Today we have many “gut microbiota” and “water microbiome” articles, as well as quite a few reviews in “Food microbiology” sector. One article (among many interesting today) I would like to highlight is the one from Guillaume Bernard and how unraveling the microbial dark matter should be identified as a central priority for biologists.

Jobs

Microbiology Technician -R&D, Lille, France

Consultant Medical Microbiologist, Birmingham, UK

Events

1st International Conference on Microbial Food and Feed Ingredients (MiFFI2018): 2-4 May 2018, Denmark

12th Vaccine Congress, Budapest, Hungary

General microbiome

Synergistic gold–copper detoxification at the core of gold biomineralisation in Cupriavidus metallidurans  – L. Bütof – Metallomics

The role of the type VI secretion system vgrG gene in the virulence and antimicrobial resistance of Acinetobacter baumannii ATCC 19606 – Jianfeng Wang – PLOS One

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria – Marike Palmer – Frontiers in Microbiology

Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery – Guillaume Bernard – Genome Biology and Evolution

Draft genome sequence of Paenibacillus strain LK1, a phytohormone producing bacterium – Kun Liu – 3 Biotech

Pregnancy and early life

Review: Urinary tract infection during pregnancy: current concepts on a common multifaceted problem – Kallirhoe Kalinderi – Journal of Obstetrics and Gynaecology

Human respiratory microbiome

In children, the microbiota of the nasopharynx and brochoalveolar lavage fluid are both similar and different – Kirsten M. Kloepfer – Pediatric Pulmonology

At the Root: Defining and Halting Progression of Early Chronic Obstructive Pulmonary Disease – Fernando J. Martinez – American Journal of Respiratory and Critical Care Medicine

Oral microbiome

Transcriptome of healthy gingival tissue from edentulous sites in patients with a history of generalized aggressive periodontitis – Tiago Taiete – Journal of Periodontology

Evaluation of oxidative status in patients with chronic periodontitis and polycystic ovary syndrome: A cross-sectional study – Ebru Saglam – Journal of Periodontology

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – Irina Marie Velsko – bioRxiv

Presence of the esp gene in Enterococcus faecium derived from oropharyngeal microbiota of haematology patients – Milica Jovanović – Archives of Oral Biology

Short-term microbiological effects of photodynamic therapy in non-surgical periodontal treatment of residual pockets: A split-mouth RCT – Mônica Grazieli Corrêa – Lasers in Surgery and Medicine

Human skin microbiome

Platelet activation and aggregation by the opportunistic pathogen Cutibacterium (Propionibacterium) acnes – Frida Petersson – PLOS One

Human vaginal microbiome

Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections – Noa Ziklo – Frontiers in Celular & Infection Microbiology

Human gut microbiome

Report: Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria – Christine M. Deje – Science

Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells – Liam Chung – Cell Host & Microbe

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis – Michael Mintz – PLOS One

Infectious bursal disease virus infection leads to changes in the gut associated-lymphoid tissue and the microbiota composition – Li Li – PLOS One

Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades – Shinichiro Hirai – PLOS One

Gut microbiome and depression: what we know and what we need to know – Gal Winter – Reviews in the Neurosciences

Connection between BMI related plasma metabolite profile and gut microbiota – Filip Ottosson – The Journal of Clinical Endocrinology & Metabolism

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – Tanya T. Nguyen – Journal of Psychiatric Research

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

Anaerobic 4-hydroxyproline utilization: discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity – Yolanda Y. Huang – Gut Microbes

Micro Integral Membrane Protein (MIMP), a Newly Discovered Anti-Inflammatory Protein of Lactobacillus Plantarum, Enhances the Gut Barrier and Modulates Microbiota and Inflammatory Cytokines – Yin M. – Cellular Physiology and Biochemistry

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations – Matthew A. Jackson – PeerJ

Animal experiments 

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin – Lance W. Noll – PLOS One

Shift of uterine microbiota associated with antibiotic treatment and cure of metritis in dairy cows – Soo Jin Jeon – Veterinary Microbiology

Microbiota-derived Metabolic Factors Reduce Campylobacteriosis in Mice  – Xiaolun Sun – Gastroenterology

Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis – Bi-Feng Yuan – Analitical Chemistry

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 One

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B.Holman – Veterinary Microbiology

IL-6-mediated signaling pathways limit Chlamydia muridarum infection and exacerbate its pathogenicity in the mouse genital tract  – Xin Sun – Microbes and Infection

Gut microbial composition can differentially regulate bile acid synthesis in humanized mice – Dae Joong Kang – Hepatology Communications

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction – Youlian Zhou – mSystems

Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents – Leore T. Geller – Molecular & Cellular Oncology

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Scientific Reports

Dietary supplementation with a nucleotide-rich yeast extract modulates gut immune response and microflora in weaned pigs in response to a sanitary challenge – S. M. Waititu – Animal

Animal microbiome 

Cellulose-dependent expression and antibacterial characteristics of surfactin from Bacillus subtilis HH2 isolated from the giant panda – Ziyao Zhou – PLOS One

Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection – Mirela D’arc – BMC Retrovirology

Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Plant, root, and soil microbiome

Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth – Gui-Hua Lu – PLOS One

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities – Eric R. Hester – mSystems

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome – Collin M. Timm – mSystems

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits – Thangasamy Saminathan – Frontiers in Plant Science

Links between nanoscale and macroscale surface properties of natural root mucilage studied by atomic force microscopy and contact angle – Robin Kaltenbach – Journal of Colloid and Interface Science

Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron – Ao-Lei He – International Journal of Molecular Science

Water and extremophile microbiome 

High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment – LuongVan Duc – Chemosphere

Establishment and convergence of photosynthetic microbial biomats in shallow unit process open-water wetlands – Zackary L.Jones – Water Research

Review: Bioactive compounds from marine macroalgae and their hypoglycemic benefits – ChaoZhao – Trends in Food Science & Technology

A Short Comparison of Two Marine Planktonic Diazotrophic Symbioses Highlights an Un-quantified Disparity – Andrea Caputo – Frontiers in Marine Science

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

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – Thea Van Rossum  – bioRxiv

Trace Metal Requirements and Interactions in Symbiodinium kawagutii – Irene B. Rodriguez – Frontiers in Microbiology

Depth-Resolved Variations of Cultivable Bacteria and Their Extracellular Enzymes in the Water Column of the New Britain Trench – Qianfeng Liu – Frontiers in Microbiology

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function – Sheila Roitman – The ISME Journal

Picoplankton distribution influenced by thermohaline circulation in the southern Adriatic – Tina Šilović – Continental Shelf Research

Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey) – Yucel-Gier – Chemistry and Ecology

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea – Shu-Xian Yu – PeerJ

Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics – Sonja Oberbeckmann – Frontiers in Microbiology

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic – Oriol Grau – Molecular Ecology

Built environment 

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting – Yanan Yin – Canadian Journal of Microbiology

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Josh – Journal of Environmental Sciences

Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics – Ryan P. Bartelme – Frontiers in Microbiology

Food microbiology

Review: Recent advances in understanding the anti-obesity activity of anthocyanins and their biosynthesis in microorganisms – Lianghua Xie – Trends in Food Science & Technology

Review: Combining reformulation, active packaging and non-thermal post-packaging decontamination technologies to increase the microbiological quality and safety of cooked ready-to-eat meat products – Claudia N.Horita – Trends in Food Science & Technology

Review: Impact of curcumin nanoformulation on its antimicrobial activity – Anderson Clayton da Silva – Trends in Food Science & Technology

Review: Antimicrobial potential of legume extracts against foodborne pathogens: A review – M.C.Pina-Pérez – Trends in Food Science & Technology

Long-term kinetics of Salmonella Typhimurium ATCC 14028 survival on peanuts and peanut confectionery products – Maristela S. Nascimento – PLOS One

Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages – Marina Giello – Food Microbiology

Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China – Zhaoxia Wang – Food Microbiology

Bacterial and fungal microbiota of spontaneously fermented Chinese products, Rubing milk cake and Yan-cai vegetable pickles – Xin Liu – Food Microbiology

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese – A. S. Bertuzzi – mSytems

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions – Nan Li – Scientific Reports

Phages and viruses

The Human Virome – Selene Zárate – Archives of Medical Research

Microreview: Contractile injection systems of bacteriophages and related systems – Nicholas M.I. Taylor – Molecular Microbiology

In vitro models for deciphering the mechanisms underlying the sexual transmission of viruses at the mucosal level – Julie Frouard – Virology

Bioinformatics

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria – Eliot C. Bush – BMC Bioinformatics

Microbes in the news

Scientists say Earth’s atmosphere is raining viruses and bacteria down on the entire planet

Medicines from engineered bacteria offer promise — and pitfalls

Microbes on the market 

uBiome, the Leader in Microbial Genomics, Launches New Research Study Allowing SmartGut™ Patients to Assess the Impact of Diet and Lifestyle on Gut Conditions

February 2, 2018

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Today’s digest is full of exciting microbiome papers and brilliant reviews, including an update on the Human Microbiome Project.

 

General Microbiome

Toward an integrative molecular approach to wildlife disease. DeCandia AL. Conservation Biology

Opinions: Genome watch: Keeping tally in the microbiome.Almeida A. Nature Reviews Microbiology

REVIEW: Cancer immunotherapy in 2017: The breakthrough of the microbiota.Kroemer G. Nature Reviews Immunology

BACTERIOPHAGES OF THE URINARY MICROBIOME.Miller-Ensminger T. Journla of Bacteriology

Gut Microbiome

REVIEW: Influence of functional food components on gut health.Wan MLY. Critical Reviews on Food Science and Nutrition

REVIEW:Gut Microbiota and the Neuroendocrine System. Farzi A. Neurotherapeutics.

Gut as an emerging organ for the treatment of diabetes.Haluzik M. Journal of Endocrinology

Human Microbiome Project

Host genetic variation and its microbiome interactions within the Human Microbiome Project.Kolde R. Genome Medicine

 Skin Microbiome

Commensal microbiota modulate gene expression in the skin.Meisel JS. Microbiome

Plant, Soil, and Water Microbiome

Effect of light wavelength on hot spring microbial mat biodiversity.Nishida A. PLos One

Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from acid mine drainage. Tardy V. Applied Microbiology and Biotechnology

Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA.Sirisena KA. Microbial Ecology

Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments. Hede N. Microbial Ecology

REVIEW:Rhizobia: from saprophytes to endosymbionts.Poole P. Nature Reviews Microbiology

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.Probst AJ, Ladd B. Nature Microbiology

Inorganic carbon addition stimulates snow algae primary productivity.Hamilton TL. ISME Journal

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. Broberg M.Microbiome

Microbes participated in macrophyte leaf litters decomposition in freshwater habitat. Zhao B. FEMS Microbiology Ecology

Animal Microbiome and Experiments

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times. Lim JS. Asian-Australasian Journal of Animal Science

Effects of dietary fiber levels on cecal microbiota composition in geese.Li Y. Asian-Australasian Journal of Animal Science

Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir. Cabral BCA. Microbiology Open

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L.Alberoni D. Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2.Yitbarek A. Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish. Legrand TPRA. Frontiers in Microbiology

Antiobitics

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan.Zhu D. Environmental Science and Technology

January 31, 2018

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Today, research in prediabetes microbiome, bacteriophages in urinary microbiota, several reviews and a good number of papers focused in animal microbiome.

 

Human Microbiome

Review: Influence of functional food components on gut health – Murphy L.Y. Wan – Critical Reviews in Food Science and Nutrition

Review: Gut Microbiota and the Neuroendocrine System – Aitak Farzi – Neurotherapeutics

Laxative effect of repeated Daiokanzoto is attributable to decrease in aquaporin-3 expression in the colon – Risako Kon – Journal of Natural Medicines

Aberrant intestinal microbiota in individuals with prediabetes – Kristine H. Allin – Diabetologia

Perspective: The Potential for Topical Probiotic Treatment of Chronic Rhinosinusitis, a Personal Perspective – Anders U. Cervin – Frontiers in cellular and infection microbiology

The third tier in treatment: Attending to the growing connection between gut health and emotional well-being – Joseph Verdino – Health psychology open

Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? – Valerio Nobili – Archives of medical science

Kynurenic Acid: The Janus-Faced Role of an Immunomodulatory Tryptophan Metabolite and Its Link to Pathological Conditions – Elisa Wirthgen – Frontiers in immunology

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis – Susana Matamouros – Proceedings of the National Academy of Sciences of the United States of America

Review: Gut as an emerging organ for the treatment of diabetes – Martin Haluzik – The Journal of endocrinology

Bacteriophages Of The Urinary Microbiome – Taylor Miller-Ensminger – Journal of bacteriology

Commensal microbiota modulate gene expression in the skin – Jacquelyn S. Meisel – Microbiome

Host genetic variation and its microbiome interactions within the Human Microbiome Project – Raivo Kolde – Genome medicine

 

Animal Microbiome

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times – Joung-Soo Lim – Asian-Australasian journal of animal sciences

Effects of different dietary ratio of metabolizable glucose and metabolizable protein on growth performance, rumen fermentation, blood biochemical indices and ruminal microbiota of 8 to 10-month-old heifers – Jie Sun – Asian-Australasian journal of animal sciences

Effects of dietary fiber levels on cecal microbiota composition in geese – Yanpin Li – Asian-Australasian journal of animal sciences

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua – Kiran G. Bapatla – Journal of Basic Microbiology

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model – J.E. Libbey – Beneficial Microbes

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L. – D. Alberoni – Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2 – A. Yitbarek – Beneficial Microbes

Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits – Y. Zhou – Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in microbiology

 

Plant/Soil Microbiome

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline – Martin Broberg – Microbiome

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan – Dong Zhu – Environmental science & technology

 

Environmental Microbiome

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

 

General Microbiome

Cross-regulatory circuit between AHR and microbiota – Jian Ji – Current Drug Metabolism

‘Massilimalia timonensis’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol – P. Afouda – New microbes and new infections

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies – Stefano Campanaro – Scientific Reports

January 28, 2018

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A preprint on the gut microbiome of few tribal groups in the Himalayan region; association between vaginal microbiota and HIV;   an integrative approach that encompasses  metatranscriptomics & fatty acid profiling to study the rumen microbiome during feeding;   environmental adaptation shapes the gut microbiota of Rhesus macaques;   microbiome of cactus rhizosphere;   news about uBiome; antibiotics;  and many more articles for today’s digest!

General microbiome

Review: Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome – S Sandoval-Motta – Archives of Medical Research

Multi-site human microbiome

The nasal microbiome mirrors and potentially shapes olfactory function – K Koskinen – Scientific Reports

Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls – Y Qiao – Scientific Reports

Human respiratory microbiome

Pseudomonas aeruginosa Biofilms: Host Response and Clinical Implications in Lung Infections – NM Maurice – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Analysis of the skin mycobiome in adult patients with atopic dermatitis – SH Han – Experimental Dermatology

Human vaginal microbiome

Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study – RS McClelland – The Lancet

Prevalence of vaginal microorganisms among pregnant women according to trimester and association with preterm birth – K-A Son – Obstetrics & Gynecology Science

Human gut microbiome

Preprint: Gut microbiome transition across a lifestyle gradient in Himalaya – AR Jha – bioRxiv

Physical exercise, gut, gut microbiota, and atherosclerotic cardiovascular diseases – J Chen – Lipids in Health and Disease

Therapeutic Opportunities in Intestinal Microbiota–Virus Interactions – V Monedero – Trends in Biotechnology

Almond Consumption and Processing Affects the Composition of the Gastrointestinal Microbiota of Healthy Adult Men and Women: A Randomized Controlled Trial. – HD Holscher – Nutrients

Effects of Ampicillin on the Gut Microbiome of an Adult Male as Determined by 16S rRNA V4 Metagenomics Sequencing and Greengenes Bioinformatics Suite – K Anukam – Journal of Advances in Microbiology

Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis – EJ Laserna-Mendieta – Journal of Crohn’s and Colitis

The Role of Bacteria, Probiotics and Diet in Irritable Bowel Syndrome – A Harper – Foods

Animal experiments 

Preprint: Inter- and intra-domain functional redundancy in the rumen microbiome during plant biomass degradation – A Soellinger – bioRxiv

Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis. – N Jiao – Physiological Genomics

Protective effect of rosmarinic acid and carnosic acid against streptozotocin-induced oxidation, glycation, inflammation and microbiota imbalance in diabetic rats. – J Ou -Food & Function

Glucocorticoids Drive Diurnal Oscillations in T Cell Distribution and Responses by Inducing Interleukin-7 Receptor and CXCR4 – A Shimba – Immunity

Review: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – TT Nguyen – Journal of Psychiatric Research

Animal microbiome 

Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment – J Zhao – Microbial Ecology

Opinion: Mission Accomplished? We Need a Guide to the ‘Post Release’ World of Wolbachia for Aedes-borne Disease Control – SA Ritchie – Cell

Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster – KL Adair – The ISME Journal

In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor – YH Jo – Entomological Research

Plant, root and soil microbiome

Editorial special issue: the soil, the seed, the microbes and the plant – EB Nelson – Plant and Soil

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid – Y Zhang – Current Microbiology

The effects of road building on arbuscular mycorrhizal fungal diversity in Huangshan Scenic Area – A Yang – World Journal of Microbiology & Biotechnology

The role of species turnover in structuring bacterial communities in a local scale in the cactus rhizosphere – VN Kavamura – Plant and Soil

p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions – X Zhou – Biology and Fertility of Soils

Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition – M Unterseher – Mycological Progress

Identification, synthesis and regulatory function of the N-acylated homoserine lactone signals produced by Pseudomonas chlororaphis HT66 – H Peng – Microbial Cell Factories

Building Bioeconomy in Agriculture: Harnessing Soil Microbes for Sustaining Ecosystem Services – R Rengalakshmi – Towards a Sustainable Bioeconomy: Principles, Challenges and Perspectives

Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology – JL Wood – Frontiers in Microbiology

Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant – E Megías – Genome Announcements

Copper Bioleaching in China: Review and Prospect – S Yin – Minerals

Water microbiome and extremophiles 

Core promoter information content correlates with optimal growth temperature – AA Aptekmann – Scientific Reports

Food microbiology

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening – M Olvera-García – Applied Microbiology and Biotechnology

Phages and viruses

Review: Phage or foe: an insight into the impact of viral predation on microbial communities – L Fernández – The ISME Journal

Techniques

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity – KJ Hoegler – Journal of Molecular Evolution

Microbes in the news

uBiome, the Leader in Microbial Genomics, Launches SmartGut and SmartJane Microbiome Test Kits in Canada – Daily Telescope

Niki Bezzant: A gutsful of good health – NZ Herald

How Phenylbutazone, Firocoxib Affect Horses’ Gut Microbiota – the Horse

Botulinum-type toxins jump to a new kind of bacteria – Science Daily

‘Forgotten’ antibiotic offers hope against worst superbugs – Digital Journal

Detect The Level Of Bacteria In Food With This Smartphone-Based System – Wonderful Engineering

When bad bugs jump from farm to bedside – Hutch News

January 26, 2018

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Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv

January 25, 2018

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Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

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Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

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

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

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Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice  – Feifei Lin – Food and Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista – British Journal of Nutrition

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

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

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

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

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Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

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

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

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Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

 

January 9, 2018

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Today, a brief digest with several reviews: microbiota in multiple sclerosis, food allergy, microbiome and diabetes, modulation of cardiovascular diseases and more. Additionally: GI tract gas analysis, SCFA effects on human, and the effect of inulin-type fructans on human microbiota.  

Human Microbiome

Review: The Local Defender and Functional Mediator: Gut Microbiome – Yang H. – Digestion

Review: Update of treatment algorithms for Clostridium difficile infection – R.E. Ooijevaar – Clinical Microbiology and Infection

Review: Gut microbiome and pediatric multiple sclerosis – Helen Tremlett – Multiple Sclerosis Journal

Review: “Evaluating Causality of Gut Microbiota in Obesity and Diabetes in Humans” – A.S. Meijnikman – Endocrine Reviews

Review: Mechanisms of food allergy – Hugh A. Sampson – Journal of Allergy and Clinical Immunology

Review: Microbial modulation of cardiovascular disease – J. Mark Brown  – Nature Reviews Microbiology

A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut – Kourosh Kalantar-Zadeh – Nature Electronics

An introduction to the microbiome and MS – Sebastien Trott – Multiple Sclerosis Journal

Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV negative MSM engaging in CRAI – Nicole Pescatore – AIDS Research and Human Retroviruses

Clinical sources and antimicrobial susceptibility of Prevotella timonensis at the university hospital of Montpellier, France – Salim Aberkane – Anaerobe

A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut – Kourosh Kalantar-Zadeh – Nature Electronics

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases – Rachel Fellows – Scientific Reports

Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan – Yung-Yu Hsieh – Scientific Reports

SCFAs strongly stimulate PYY production in human enteroendocrine cells – P. Larraufie – Scientific Reports

Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota – Aurélie Durand – Nature Communications

 

Animal Microbiome

Evaluation of the effects of different diets on microbiome diversity and fatty acid composition of rumen liquor in dairy goat – P. Cremonesi – Animal

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys – Pål Trosvik – Scientific Reports

Dietary soybean meal affects intestinal homoeostasis by altering the microbiota, morphology and inflammatory cytokine gene expression in northern snakehead – Shuyan Miao – Scientific Reports

 

Food Microbiome

Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems – Marie Frétin – Scientific Reports

 

Beneficial Microbes and Beneficial Compounds

Tetraglochin cristatum (Britton) Roth: a medicinal plant from the Argentinean highlands with potential use in vaginal candidiasis – María Alejandra Moreno – Journal of Ethnopharmacology

Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study – Genelle Healey – British Journal of Nutrition

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan – Toshitaka Odamaki – Scientific Reports

 

Extremophiles

Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll – Junichi Miyazaki – Royal Society Open Science

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology