Category Archives: Events and jobs

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 1, 2018

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The publication of a Springer manual entitled Mechanisms underlying host-microbiome interactions in pathopysiology of human diseases contains multiple interesting articles today, including reviews on the gut microbiome and preterm infant gut development, colerectal cancer, and metabolic disease, as well as a useful review of statistical models for mouse and human microbiome data. In addition, a revisitation of gut enterotypes via metabolomics, decreased Akkermansia muciniphila in psoriasis,  the bacterial communities of fiddler crabs, the impact of different wavelengths of light on hot spring bacteria, and two articles on the uses of metabarcoding in both 16S and eukaryotic microbiota analysis.

Events and jobs

Microbiology Manager – Covance – Indianapolis, Indiana

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Pregnancy and early life

*Review: Impact of Microbes on the Intestinal Development of the Preterm Infant – Elizabeth Humphrey – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Multi-site human microbiome

Review: Good and Bad Farming: The Right Microbiome Protects from Allergy – Markus Johannes Ege – Allergy Prevention and Exacerbation

Human gut microbiome

*Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes – Manoj Kumar Verma – Scientific Reports

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – BMC Gasteroentrology

*The Akkermansia muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Review: The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer – Cheng-Bei Zhou – Critical Reviews in Microbiology

Editorial: Unveiling the gut virome in human health and diseases – Tao Zuo – International Journal of Clinical Virology

*Review: The Influence of the Microbiota on the Etiology of Colorectal Cancer – Melissa C. Kordahi – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*Review: Altered Microbiota and Their Metabolism in Host Metabolic Diseases – Beng San Yeoh –  In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Review: The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All? – Eva Untersmayr – Allergy Prevention and Exacerbation

*Review: Fecal Microbiota Transplants: Current Knowledge and Future Directions – Roxana Chis – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

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Animal experiments

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice – Ann Wells – Journal of Proteome Research

The Changes of Colonic Bacterial Composition and Bacterial Metabolism Induced by an Early Food Introduction in a Neonatal Porcine Model – Chao Shi – Current Microbiology

Animal microbiome

*Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Transcriptional changes detected in fecal RNA of neonatal dairy calves undergoing a mild diarrhea are associated with inflammatory biomarkers – Fernanda Rosa – PLOSone

Tiny but mighty: The role of the rumen microbes in livestock production
K M Cammack – Journal of Animal Science

Effects of Spray-Dried Porcine Plasma on Fecal Microbiota in Nursery Pigs – Huyen Tran – Journal of Animal Science

Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows – Susakul Palakawong Na Ayudthaya – Biotechnology for Biofuels

Plant, root, and soil microbiome

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production – Reeta Goel – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 7. Springer

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire – Taylor K. Dunivin – PLOSone

Review: The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance – Msizi Mhlongo – Frontiers in Plant Science

Characterization of bacteria isolated from the Saffron (Crocus Sativus L.) rhizosphere – Majid Jami Al-Ahmadi – Journal of Horticultural Research

Review: Rhizoremediation – Plant Microbe Interactions in the Removal of Pollutants – Mehak Oberai – International Journal of Current Microbiology and Applied Sciences (IJCMAS)

Role of microbes in organic carbon decomposition and maintenance of soil ecosystem – Hina Khatoon – International Journal of Chemical Studies

Water and extremophile microbiome

Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing – Kazuhisa Okada – Scientific Reports

*Effect of light wavelength on hot spring microbial mat biodiversity – Akifumi Nishida – PLOSone

Microbial Ecology

Estimating taxon-specific population dynamics in diverse microbial communities – Benjamin J. Koch – Ecosphere

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains – Eric Hong Jian Wong – Scientific Reports

Resistome

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut – Lisa Ciesinski – PLOSone

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Probiotics / prebiotics

An Integrative Review on the Effect of Prebiotics, Probiotics, and Synbiotics on Infection After Colorectal Cancer Surgery – Sarah Williams Anderson – Aorn Journal

Phages and Viruses

Metagenomic Analysis of the Jinding Duck Fecal Virome – Lili Zhao – Current Microbiology

Bioinformatics

*Statistical Models and Analysis of Microbiome Data from Mice and Humans – Yinglin Xia – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases – Qingyu Chen – Journal of Data and Information Quality

Techniques

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

*16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer) – Clare Bird – PLOSone

*Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients – Ibrahim Hamad – PLOSone

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Microbes in the news

The Germ and the Gene: Gut Bacteria Research Takes a Step Forward – Ruairi MacKenzie – Technology Networks

These bacteria produce gold by digesting toxic metals – EurekaAlert

 

 

January 27, 2018

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A Saturday digest with lots of fun and weird news of microbiome!
Events and jobs

Adjunct Faculty- Biology, Microbiology, Anatomy & Physiology – St. Louis Community College in Missouri – USA

General microbiome

A Case of Recurrent Pasteurella Bacteremia in an Immunocompetent Patient with No Animal Bite. – F Zarlasht – The American Journal of Case Reports

Pregnancy and early life

Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. – EM Fricke – American Journal of Reproductive Immunology

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants – RD Zwittink – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach – FM Borges – Current Microbiology

Review: Dietary practices and FODMAPs in South Asia: Applicability of the low FODMAP diet to patients with irritable bowel syndrome – SP Hewawasam – Journal of Gastroenterology and Hepatology

Animal experiments 

Preprint: Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. – D Fast – bioRxiv

Beneficial effects of Rifaximin in post-infectious irritable bowel syndrome mouse model beyond gut microbiota – Y Jin –  Journal of Gastroenterology and Hepatology

Plant, root and soil microbiome

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. – EJ Canter – Ecology

Purple corn-associated rhizobacteria with potential for plant growth promotion – A Castellano-Hinojosa – Journal of Applied Microbiology

Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease – OY de Assis Costa – PLoS One

Biosynthetic and antimicrobial potential of actinobacteria isolated from bulrush rhizospheres habitat in Zhalong Wetland, China – Y Li – Archives of Microbiology

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil – M Pacwa-Płociniczak – Water, Air and Soil Pollution

Water microbiome and extremophile 

Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids – H Bestová – Oecologia

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide –  A Nishihara – J-Stage

Food microbiology

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing – HNJ Shangpliang – Scientific Reports

Phages and viruses

Preprint: Diversity and evolution of the emerging Pandoraviridae family – M Legendre – bioRxiv

Microbes in the news

Explore the human microbiome in new Delaware natural history museum exhibit – Delaware Public Media

Thoroughness of panel called into question – Delta Optimist

When DNA Went Mobile Some Archaea Jumped Out of the Hot Tub – GEN News

Scientists find 10 new defense systems used by bacteria – Science News

ASTRONAUTS LIVING IN SPACE CAN EAT BACTERIA THAT FEED ON HUMAN WASTE – Newsweek

A Never-Before-Seen Virus Was Just Found in the Sea, and It Kills Bacteria – Inverse Science

Bacteria block transmission of Zika and Dengue viruses – Medical Xpress

First annual thesis competition held at JMU – The Breeze

Microbiome research refines HIV risk for women – EurekAlert

Shimmery bacteria plus a canvas equals art, briefly – Chicago Tribune

BACTERIA THAT HITCH RIDES ON TOOTHBRUSHES, DIAPERS AND OTHER PLASTIC POLLUTION ARE KILLING CORAL REEFS – Newsweek

 

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 23, 2018

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After the US government shutdown, today’s Digest features several human gut microbiome, food microbiology papers and many news pieces. There are some other highlights as well. A large longitudinal experiment in a tropical rain forest examines how soil microbes adapt genetically to nutrient changes in the soil. A synthetic enzyme rescues E. coli in iron-limited medium. Open access from high impact medical journals is still lacking.

Jobs and events

Digital Communications Officer – Microbiology Society – London

Keystone Symposium on Natural Products and Synthetic Biology

General microbiology

Sequence-based classification and identification of Fungi – David Hibbett et al. – Mycologia

Preprint: E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li et al. – bioRxiv

* A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli – Ann E Donnelly et al. – Nature Chemical Biology

Press: A randomly generated, totally novel enzyme rescues mutant bacteria – Diana Gitig – ArsTechnica

Annotations of Microbacterium foliorum – Debbie Jacobs-Sera – Sea Phages

Human gut microbiome

Reoccurring review (no abstract available): Letter to the Editor: Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Andre Alonso Taco-Masias and Augusto Rafael Fernandez-Aristi – Obesity Surgery

Also see a previous review: Influence of intestinal microbiota on body weight gain: a narrative review of the literature – Camila S. Cardinelli et al. – Obesity Surgery

Impact of intestinal mannitol on hyperammonemia, oxidative stress and severity of hepatic encephalopathy in the ED – Daniel H. Montes-Cortés et al. – The American Journal of Emergency Medicine

Clostridial strain-specific characteristics associated with necrotizing enterocolitis – Sophia Schönherr-Hellec et al. – Applied and Environmental Microbiology

Intestinal dysbiosis and permeability: the yin and yang in alcohol dependence and alcoholic liver disease – Peter Stärkel et al. – Clinical Science

In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way – Thaisa MoroCantu-Jungles et al. – Carbohydrate Polymers

Animal microbiome

In vitro: Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure – E.G. Ozbayram et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

* Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil – Qiuming Yao et al. – Nature Ecology and Evolution

Press: Researchers reveal how microbes cope in phosphorus-deficient tropical soil – Sara Shoemaker – Phys.org

Water and extremophile microbiome

Bacterial community changes in copper and PEX drinking water pipeline biofilms under extra disinfection and magnetic water treatment – J. Inkinen et al. – Journal of Applied Microbiology

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – M. Salomez et al. – Journal of Applied Microbiology

Lead-resistant bacteria from Saint Clair River sediments and Pb removal in aqueous solutions – Nichole Bowman et al. – Applied Microbiology and Biotechnology

Food microbiology

Ultrasound improves antimicrobial effect of sodium dichloroisocyanurate to reduce Salmonella Typhimurium on purple cabbage – Ana Lúcia Almeida Duarte et al – International Journal of Food Microbiology

Characterization of the spoilage potential of pure and mixed cultures of bacterial species isolated from tropical yellowfin tuna (Thunnus albacares) – A. Silbande et al. – Journal of Applied Microbiology

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year – L.M. Broissin-Vargas et al. – Journal of Applied Microbiology

An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England – C. Willis et al. – Journal of Applied Microbiology

Microbes in the news

Bacteria warning for Kapiti waterways – Newshub

Common salt kills rat fever bacteria? Public health experts say it can – TNN – Times of India

Editorial: Vendors’ ultimatum will save us from cholera, typhoid – The Standard

Why Flesh-Eating Bacteria Can Look Like the Flu – Rachael Rettner – Live Science

Geologists find bacteria that takes traces of gold and turns them into nuggets – Eliza Goetze – ABC News

Shigella Bacteria Diarrhea in Children: Should WHO Guidelines Be Modified? – Julie McShane – Medical News Bulletin

* Chemical ‘aphrodisiac’ jumpstarts the sex life of a single-celled organism – Brianna Abbott – Science Line

Microbiome predicts blood infections in pediatric cancer patients – EurekAlert

Dietary Fiber Protects Against Obesity and Metabolic Syndrome, Study Finds – Georgia State University News Hub

How climate change weakens coral ‘immune systems’ – EurekAlert

* Early changes in brain immunity may underlie sex bias in autism – Nicholette Zeliadt – Spectrum

Detecting Zoonotic Protists In Raw Sewage For Environmental Monitoring – Steven Sullivan – Science Trends

Microbes on the market

Synspira Therapy Eliminates Antibiotic-resistant Lung Bacteria, Study Shows – Marta Figueiredo – Cystic Fibrosis News Today

Microbiome Sequencing Service Market – Baseclear, Clinical-Microbiomics, MR DNA (Molecular Research Lp), Molzym, Zymo Research, Rancho Biosciences, Microbiome Therapeutics, Microbiome Insights, Openbiome, Resphera Biosciences, Shanghai Realbio Technology – Oscar – Hugo Press

VALBIOTIS Announces a Significant Effect of VALEDIA® on Intestinal Microbiota – Business Wire

Publishing and education

* Preprint: Open access policies of high impact medical journals: a cross-sectional study – Time Ellison et al. – bioRxiv

 

January 22, 2018

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Quite a short digest today, still many interesting articles. Today I would like to focus on two papers, both related to  water microbiome. In the first one Antonio M. Martin-Platero et al.  show how microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp, while the paper by Yoann Seeleuthner et al. reveals underestimated functional diversity of  uncultured marine protists across oceans. The third paper I would like to mention is a report by Manuel Delgado-Baquerizo, which provides a global atlas of the dominant bacteria found in soil.

Jobs

Research Technician, Newcastle University, UK

Research Technician (Microbiology & Microbial Genetics), Newcastle University, UK

Postdoc position in the Antimicrobial Resistance Unit, University Complutense of Madrid – UCM, Madrid, Spain

General microbiome

E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li – bioRxiv

Oral microbiome

Clinical and microbiological evaluation of the effect of Lactobacillus reuteri in the treatment of mucositis and peri-implantitis: A triple-blind randomized clinical trial – M. Galofré – Journal of periodontal research

 

Human gut microbiome

Intestinal Epithelial Cell–Derived LKB1 Suppresses Colitogenic Microbiota – Xia’nan Liu – The Journal of Immunology

Microbial regulation of the L cell transcriptome – Tulika Arora – Scientific Reports

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study – Yang Shen – Schizophrenia Research

1-Day or 5-Day Fecal Samples, Which One is More Beneficial to be Used for DNA-Based Gut Microbiota Study – Tingting Su – Current Microbiology

16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones – Ruiqiang TangYonghua Jiang – Urolithiasis

Structural characterization and in vitro fermentation of a novel polysaccharide from Sargassum thunbergii and its impact on gut microbiota – Xiong Fu – Carbohydrate Polymers

Oral Administration of Compound Probiotics Ameliorates HFD-Induced Gut Microbe Dysbiosis and Chronic Metabolic Inflammation via the G Protein-Coupled Receptor 43 in Non-alcoholic Fatty Liver Disease Rats – Yinji Liang – Probiotics and Antimicrobial Proteins

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

Plant, root, and soil microbiome

Report: A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science

Water and extremophile microbiome 

Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River – Tang Liu – BMC Microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.del R.Mora-Ruiz – Systematic and Applied Microbiology

High resolution time series reveals cohesive but short-lived communities in coastal plankton – Antonio M. Martin-Platero – Nature Communication

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans – Yoann Seeleuthner – Nature Communications

Microbes in the news 

New type of steel kills bacteria with … nanoparticles!

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago

January 21, 2018

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A light reading for Sunday!
Events and jobs

Professor (Chairperson), Department of Microbiology and Immunology (MIC) – The Uniformed Services University of the Health Sciences – Bethesda, Maryland

Postdoc in Intestinal Microbiology and Ecology – The National Food Institute (DTU Food) – Denmark

SCIENCE INQUIRY LECTURE: “FLYING” BACTERIA AS POTENTIAL RAINMAKERS – APRIL 18, 2018; 7:00PM – 8:30PM – HAGER AUDITORIUM, Montana 

General microbiome

Review: Bacterial RNA Biology on a Genome Scale – Jens Hör  – Molecular Cell

Multi-site human microbiome

Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye – Xiaofeng Wen – Progress in Retinal and Eye Research

Human skin microbiome

The role of fatty acids and their endocannabinoid-like derivatives in the molecular regulation of appetite – Renger F. Witkamp – Molecular Aspects of Medicine

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair – Jonathan L. Linehan – Cell

Propionibacterium acnes Strains Differentially Regulate the Fate of Th17 Responses in the Skin – Emmanuel Contassot – Journal of Investigative Dermatology

Human gut microbiome

P038 FECAL MICROBIOTA TRANSPLANT (FMT) FOR IMMUNO-CHECKPOINT INHIBITOR-INDUCED COLITIS (ICI-C) IN A 50 YEAR OLD FEMALE WITH BLADDER CANCER – Yinghong Wang – Gastroenterology

P110 STEROID-RESISTANCE AND STEROID-DEPENDENCE IN INFLAMMATORY BOWEL DISEASE CAN BE LINKED WITH GUT MICROBIOTA COMPOSITION CHANGES – Natalia Danilova – Gastroenterology

P069 LOW FAT DIET IMPROVES QUALITY OF LIFE AND CHANGES THE MICROBIOME IN A CATERED, CROSS-OVER DESIGN INTERVENTION OF UC PATIENTS WITH QUIESCENT DISEASE: RESULTS OF A PILOT STUDY – Matthew C. Phillips  – Gastroenterology

Animal experiments 

The family Coriobacteriaceae is a potential contributor to the beneficial effects of Roux-en-Y gastric bypass on type 2 diabetes – Haijun Liu – Surgery for Obesity and Related Diseases

P039 FECAL MIRNAS SHAPE THE INTESTINAL MICROBIOTA – Emilie Viennois – Gastroenterology

P125 TLR4 ACTIVATION UPREGULATES EXPRESSION OF OXIDATIVE ENZYMES: IMPLICATIONS FOR INTESTINAL TUMORIGENESIS AND LUMINAL MICROBIOTA – Juan F. Burgueno – Gastroenterology

Effect of live yeast supplementation on gastric ecosystem in horses fed a high-starch diet – Samy Julliand – Livestock Science

The symbiont Lactobacillus plantarum causes intestinal pathogenesis in adult Drosophila. – David Fast – bioRxiv

Plant, root and soil microbiome

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation – Chao Ai – Geoderma

Microbial degradation of poly(ε-caprolactone) in a coastal environment – Miwa Suzuki – Polymer Degradation and Stability

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape – Sergio E. Morales – Applied Soil Ecology

Food microbiology

Polyphasic identification of Penicillia and Aspergilli isolated from Italian grana cheese – Simone Decontardi – Food Microbiology

Phages and viruses

Bacteriophages as modulator for the human gut microbiota: Release from dairy food systems and survival in a dynamic human gastrointestinal model – Meike Samtlebe – LWT

Techniques

Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population – Prathik K Vijay Kumar – bioRxiv

P168 WHERE WILL FECAL MICROBIOTA TRANSPLANTATION FIT IN THE TREATMENT ALGORITHMS FOR CROHN’S DISEASE AND ULCERATIVE COLITIS: A SYNTHESIS OF COMPLETED, ONGOING AND FUTURE TRIALS – Yiran Song – Gastroenterology

Microbes in the news

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago – Mental Floss

IIT Delhi develops a novel platform to test drug sensitivity in bacteria – The Hindu

Scientists Unlock Key Information About the World’s Soil Microbes – Yale Environment 360

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