Category Archives: Built Environment Microbiology

November 8, 2017

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Photosynthesizing bacteria printed on paper, investigations of microbial communities in water dispensers and mines, a review on the health benefits of natural products from truffles.

Human respiratory microbiome

Review: Airway Microbiota and Allergic Diseases: Clinical Implications – Eman M Fouda – International Journal of Pulmonary and Respiratory Sciences

Human oral microbiome

Proton pump inhibitor alters oral microbiome in gastrointestinal tract of healthy volunteers – Tsuyoshi Mishiro – Journal of Gastroenterology and Hematology

Human gut microbiome

Gut Microbiota Interacts with Markers of Adipose Tissue Browning, Insulin Action and Plasma Acetate in Morbid Obesity – José María Moreno-Navarrete – Molecular Nutrition and Food Research

Is there a relationship between intestinal microbiota, dietary compounds, and obesity? – Joanna Kałużna-Czaplińska – Trends in Food Science and Technology

Animal experiments

Combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota – Le Zhao – Food and Function

Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis – Fionn Dunphy Doherty – Brain, Behavior, and Immunity

Host-microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice – Antonio Molinaro – Molecular Metabolism

Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis – June-Chul Lee – PLOS ONE

Animal microbiome

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica) – Huan Li – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere – Zeno Varanini – Plant and Soil

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface – J R Halliwell – Scientific Reports

Co-existence of Rhizobia and Diverse Non-Rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii，Rhizobium multihospitium–like and Burkholderia pyrrocinia–like Strains – Junkun Lu – Frontiers in Microbiology

Diversity of endophytic bacteria from Piper spp. with antagonistic property against Phytophthora capsici causing foot rot disease in black pepper (Piper nigrum L.) – Nadiya Kollakkodan – Journal of Tropical Agriculture

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests – Sten Anslan – Soil Biology and Biochemistry

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Resource availability underlies the plant-fungal diversity relationship in a grassland ecosystem – Lauren C Cline – Ecology

Water and extremophile microbiome

Microflora Thermarum Atlas project: biodiversity in thermal spring waters and natural SPA pools – F Valeriani – Water Science and Technology: Water Supply

Modes of carbon xation in an arsenic and CO2-rich shallow hydrothermal ecosystem – Nolwenn Callac – Scientific Reports

Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea – Tiantian Yu – Applied Microbiology and Biotechnology

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula – Catherine M Luria – Frontiers in Microbiology

Built environment

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine – Yanping Bao – Science of the Total Environment

Investigation of microbial communities in water dispensers – Sangjung Park – Applied Biological Chemistry

Food microbiology

Review: Potential health benefits of natural products derived from truffles: A review – Seema Patel – Trends in Food Science and Technology

Probiotics/prebiotics

Review: The development of seaweed-derived bioactive compounds for use as prebiotics and nutraceuticals using enzyme technologies – Suvimol Charoensiddhi – Trends in Food Science and Technology

Phages and viruses

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes – Judith Villager – The ISME Journal

Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures – Joana Oliveira – Journal of Dairy Science

Bioinformatics

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks – Zhu Chengsheng – Nucleic Acids Research

Metabolomics

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database – Wailing Huang – Nucleic Acids Research

mVOC 2.0: a database of microbial volatiles – Marie C Lemfack – Nucleic Acids Research

Techniques

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems – Karsten Karczewski – Limnologica Ecology and Management of Inland Waters

More microbes

Review: Our microbes not only produce antibiotics, they also overproduce amino acids – Sergio Sanchez – The Journal of Antibiotics

Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria – José A Gutiérrez-Barranquero – Microbial Biotechnology

Microbes in the news

Bacteria-Activated Wallpaper that Generates Electricity – Katharine Keane – Architect Magazine

US government approves ‘killer’ mosquitoes to fight disease – Emily Waltz – Nature News

Bacteria may help babies’ digestive tracts more than suspected, scientists find – EurekAlert

Using neutrons to study how resistant bacteria evolve – Phys Org

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer – News Medical Life Sciences

New model reveals possibility of pumping antibiotics into bacteria – EurekAlert

Microbes on the market

Seres Therapeutics Awarded Grant from CARB-X to Support Development of Microbiome Therapeutic Candidate – Business Wire

Michael J. Fox Foundation, 23andMe to Jointly Advance Parkinson’s Disease Research – Carolina Henriques – Parkinson’s News Today

October 28, 2017

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A huge Saturday digest (150+ alerts), with many articles in the gut and animal microbiome.

Events and jobs
Postdoctoral researcher in Human Microbiome-Immune System Interactions – University of Luxembourg

Microbiome in Sexual, Maternal and Child Health Symposium – November 29, 2017

Pregnancy and early life
Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum – Sayyid Hasan – Acta Obstetricia et Gynecologica Scandivanica

The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux-A Prospective Longitudinal Interventional Study –
Christoph Castellani – Frontiers in Cellular and Infection Microbiology

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – PLoS One

2 articles on iron supplements in the American Journal of Nutrition:
Review: Effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review – Daniela Paganini – American Journal of Clinical Nutrition

Review: Excess iron intake as a factor in growth, infections, and development of infants and young children – Bo Lönnerdal – American Journal of Clinical Nutrition

Human skin microbiome
RNase 7 participates in cutaneous innate control of Corynebacterium amycolatum – Stephanie Walter – Scientific Reports

FKBP12-Dependent Inhibition of Calcineurin Mediates Immunosuppressive Antifungal Drug Action in Malassezia – Giuseppe Ianiri – mBio

Human oral microbiome
Changes in periodontal and microbial parameters after the space maintainers application – M Aydinbelge – Nigerian Journal of Clinical Practice

Microbiome associated with dentures malodour – Shai Yitzhaki – Journal of Breath Research

Human gut microbiome
Gut microbiomes of mobile predators vary with landscape context and species identity – Julia Tiede – Ecology and Evolution

Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells – Urmi Roy – Cell Reports

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile – Soobin Yoon – Journal of Microbiology

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease – Elizaveta S. Leshchiner – PNAS

Guiding longitudinal sampling in IBD cohorts – Yoshiki Vázquez-Baeza – Gut
Paper referenced: A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Distinctive Gut Microbiota Is Associated with Diarrheagenic Escherichia coli Infections in Chilean Children – Pablo Gallardo – Frontiers in Cellular and Infection Microbiology

Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis – Julia Manasson – Arthritis and Rheumatology

Severe intestinal dysbiosis is prevalent in primary Sjögren’s syndrome and is associated with systemic disease activity – Thomas Mandl – Arthritis Research and Therapy

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

Review: Visceral Congestion in Heart Failure: Right Ventricular Dysfunction, Splanchnic Hemodynamics, and the Intestinal Microenvironment – Vincenzo B. Polsinelli – Current Heart Failure Reports

Review: Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis – Gregory J. Grosicki – Calcified Tissue International

Animal experiments
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota – Nathan P. Manes – MSystems

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice – Lena Böhm – PLoS Pathogens

Clinical Effect of IRT-5 Probiotics on Immune Modulation of Autoimmunity or Alloimmunity in the Eye – Jaeyoung Kim – Nutrients

Periodontal pathogenic bacteria, Aggregatibacter actinomycetemcomitans affect non-alcoholic fatty liver disease by altering gut microbiota and glucose metabolism – Rina Komazaki – Scientific Reports

β-Glucans in food modify colonic microflora by inducing antimicrobial protein, calprotectin, in a Dectin-1-induced-IL-17F-dependent manner – T Kamiya – Mucosal Immunology

Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids – A Cait – Mucosal Immunology

Effects of direct-fed microorganisms and enzyme blend co-administration on intestinal bacteria in broilers fed diets with or without antibiotics – T E Askelson – Poultry Science

16S rDNA analysis of the effect of fecal microbiota transplantation on pulmonary and intestinal flora – Tianhao Liu – 3 Biotech

Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster – Berra Erkosar – mBio

Characterization of fecal fat composition and gut derived fecal microbiota in high-fat diet fed rats following intervention with chito-oligosaccharide and resistant starch complexes – Wenting Shang – Food and Function

Genetic ablation of Cyp8b1 preserves host metabolic function by repressing steatohepatitis and altering gut microbiota composition – Jay V Patankar – American Journal of Physiology – Endocrinology and Metabolism

Effects of a probiotic (SLAB51™) on clinical and histologic variables and microbiota of cats with chronic constipation/megacolon: a pilot study – G. Rossi – Beneficial Microbes

Bacteriocin biosynthesis contributes to the anti-inflammatory capacities of probiotic Lactobacillus plantarum – X. Yin – Beneficial Microbes

Animal microbiome
Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition – Jessy Praet – Environmental Microbiology

Bacterial community of a spider, Marpiss magister (Salticidae) – Lihua Zhang – 3 Biotech

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef – S Shamim – FEMS Microbiology Ecology

RECRUITMENT AND ESTABLISHMENT OF THE GUT MICROBIOME IN ARCTIC SHOREBIRDS – Kirsten Frond – FEMS Microbiology Ecology

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation – Tina Keller-Costa – FEMS Microbiology Ecology

Inheritance and Establishment of Gut Microbiota in Chickens – Jinmei Ding – Frontiers in Microbiology

Diversity and Transmission of Gut Bacteria in Atta and Acromyrmex Leaf-Cutting Ants during Development – Mariya Zhukova – Frontiers in Microbiology

Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.) – Carola E. Dehler – Scientific Reports

Plant, root, and soil microbiome
Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice – Denver I. Walitang – BMC Microbiology

Pseudomonas syringae pv. syringae B728a Regulates Multiple Stages of Plant Colonization via the Bacteriophytochrome BphP1 – Regina McGrane – mBio

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project – David J. Weston – New Phytologist

Bacterial Synergism in Lignocellulose Biomass Degradation – Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source – Larisa Cortes-Tolalpa – Frontiers in Microbiology

Modulation of the efficiency of trace metal phytoremediation by Sedum plumbizincicola by microbial community structure and function – Jinyu Hou – Plant and Soil

Water and extremophile microbiome
Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc – Christos A. Christakis – Extremophiles

Variability in carbon uptake and (re)cycling in Antarctic cryptoendolithic microbial ecosystems demonstrated through radiocarbon analysis of organic biomarkers – A. L. Brady – GE Biology

High reactivity of deep biota under anthropogenic CO2 injection into basalt – Rosalia Trias – Nature Communications

Editorial: Marine microbiome as source of natural products – Fernando de la Calle – Microbial Biotechnology

Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment – Lauren B. Stadler – Microbial Biotechnology

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments – Shiling Zheng – Journal of Microbiology

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments – Ke Qin – Pathogens

Review: Methods of ammonia removal in anaerobic digestion: a review – Niclas Krakat – Water Science and Technology

Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions – Hanna Fasca – Microbiology Open

Built environment
The York Gospels: a 1000-year biological palimpsest – Matthew D. Teasdale – Royal Society Open Science (sequencing of parchment)

Conductive properties of methanogenic biofilms – Cheng Li – Bioelectrochemistry

Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems – Huihui Zhou – Biotechnology for Biofuels

Microbes in space
Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission – Kaisa Koskinen – Microbiome

Food microbiology
Safety assessment of transgenic canola RF3 with bar and barstar gene on Sprague-Dawley (SD) rats by 90-day feeding test – Tianqi Lang – Regulatory Toxicology and Pharmacology

Review: The role of wine and food polyphenols in oral health – Adelaida Esteban-Fernández – Trends in Food Science & Technology

Review: The agri-food chain and antimicrobial resistance: A review – John A. Hudson – Trends in Food Science & Technology

Review: Food derived anti-adhesive components against bacterial adhesion: Current progresses and future perspectives – Xiaohong Sun – Trends in Food Science & Technology

Probiotics / prebiotics / antibiotics
Effect of a yoghurt drink containing Lactobacillus strains on bacterial vaginosis in women – a double-blind, randomised, controlled clinical pilot trial – C. Laue – Beneficial Microbes

Bifidobacterium longum BB536 alleviated upper respiratory illnesses and modulated gut microbiota profiles in Malaysian pre-school children – A.S.-Y. Lau – Beneficial Microbes

Prebiotics for the prevention of allergies: A systematic review and meta-analysis of randomized controlled trials – C. Cuello-Garcia – Clinical and Experimental Allergy

Review: Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms – Simon A Dingsdag – Journal of Antimicrobial Chemotherapy

Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms – Brett M. Babin – mBio

Phages and viruses
Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone – Frank O. Aylward – PNAS

Bioinformatics
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs – Dinghua Li – BMC Bioinformatics

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies – Alex L. Mitchell – Nucleic Acids Research

Techniques
A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – Behnoushsadat Ghodsalavi – PLoS One

New Genomes
Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics – El hadji Seck – Microbiology Open

Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory – Kevin Egan – Genome Announcements

Microbes in the news
Doctors warn new parents: Step away from the vaginal fluid swabs – Beth Mole – ARS Technica

New study details bacteria’s ‘sense of touch’ – Brooks Hays – UPI
Paper: Obstruction of pilus retraction stimulates bacterial surface sensing – Courtney K. Ellison – Science

T-Cell Enzyme Uses Deadly Multipronged Attack on Bacteria – GEN News
Paper: Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program – Farokh Dotiwala – Cell

Gut bacteria could determine whether you develop PTSD – Sian Bradley – Wired (Paper from July 19)

Gut bacteria bolster disease research in labs – UNC Health Care

The Next Big Performance Enhancing Drug: Bacteria From Elite Athletes’ Guts? – Peter Audrey Smith – Men’s Journal

Microbes on the market
French Biotech’s Crohn’s Candidate Glides Through Phase I – Alex Dale – Lab Biotech

Enterome’s EB8018, a First-in-class Drug Candidate Targeting Crohn’s Disease, Successfully Completes Phase I Study in Healthy Volunteers – Enterome – Cision (same as above link, more detail)

October 22, 2017

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A wide range of interesting articles today on the mouth, respiratory and gut microbiomes: Airway microbiota and obstruction in asthma, the tongue microbiome and pneumonia in the elderly, gut microbiome interactions with host G-protein coupled receptors, the effects of prebiotics and milk oligosaccharides on the mouse gut metabolome and stressor induced immune alterations, the impact of social stress on the gut microbiome and the host gut transcriptome, the impact of a Bacteroides integrase in a mouse model of colitis, and evidence that oral bacteria can colonize the gut in genetically and dysbiotic susceptible mice, leading to increased gut inflammation. 

  • Events and jobs

Postdoctoral Researcher in Microbiome Bioinformatics – Karolinska Institutet

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  • Human respiratory microbiome

Different Functional Genes of Upper Airway Microbiome Associated with Natural Course of Childhood Asthma – Bong-Soo Kim – European Journal of Allergy and Clinical Immunology

*Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction – Benjamin A. Turturice – PLOSone

  • Human oral microbiome

*Relationships of variations in the tongue microbiota and pneumonia mortality in nursing home residents – Shinya Kageyama – Journal of Gerontology

  • Human gut microbiome

Review: Host-Microbe Interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

Development of severe bronchopulmonary dysplasia is associated with alterations in fecal volatile organic compounds – Daniel J C Berkhout – Pediatric Research

Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health – Barbara A. Williams – International Journal of Molecular Sciences

Review: Food allergy: The influence of breast-feeding and gut microbiota – S. Hazebrouck – Revue Française d’Allergologie

Review: Whole cereal grains and potential health effects: Involvement of the gut microbiota – Lingxiao Gong – Food Research International

Review: Probiotic strains and mechanistic insights for the treatment of type 2 diabetes – Christiane S. Hampe – Endocrine

Review: Early-Life Gut Dysbiosis: A Driver of Later-Life Fibrosis? – Karen J. Ho – Journal of Investigative Dermatology

Review: Nutritional programming by glucocorticoids in breast milk: targets, mechanisms and possible implications – Jonneke J. Hollanders – Best Practice & Research Clinical Endocrinology & Metabolism

Review: Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBioMedicine

  • Fecal Transplants

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis – P. Kump – Alimentary Pharamacology and Therapeutics

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  • Animal experiments

* Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

*Stressor-induced immunomodulation is attenuated by prebiotics and milk oligosaccharides: Role of the colonic metabolome – M. Bailey – Brain, Behavior, and Immunity

*The colonic epithelial transcriptome and intestinal microbiome are significantly changed by social stressor exposure – A.R. Mackos – Brain, Behavior, and Immunity

*A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis – Roopa Hebbandi Nanjundappa – Cell

Metformin Alters Upper Small Intestinal Microbiota that Impact a Glucose-SGLT1-Sensing Glucoregulatory Pathway – Paige V. Bauer – Cell Metabolism

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota – Andréa de Andrade Rangel de Freitas – Science of The Total Environment

Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice – Takuya Kuno – Molecular Pharmaceutics

Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population – P. Villette – Epidemiology & Infection

High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community – Debora Garzetti – Genome Announcements

  • Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance – Stephan P. Rosshart – Cell

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations – Lhermie Guillaume – Foodborne Pathogens and Disease

  • Forensic Microbiome

Successive bacterial colonisation of pork and its implications for forensic investigations – Jessica Handke – Forensic Science International

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification – Sarah E. Schmedes – Forensic Science International: Genetics

  • Plant, root, and soil microbiome

Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa – P.C. Carmichael – Journal of Applied Microbiology

Mycorrhizae, invasions, and the temporal dynamics of mutualism disruption – Sara Grove – Journal of Ecology

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter – Quan YuanSoil Biology and Biochemistry

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

  • Waste and Pollution 

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community – Evangelia S. Papadopoulou – Environmental Pollution

  • Built environment

Human health risks for Legionella and Mycobacterium avium complex (MAC) from potable and non-potable uses of roof-harvested rainwater – Kerry A.Hamilton – Water Research

  • Techniques

Optimization of GC/TOF MS analysis conditions for assessing host-gut microbiota metabolic interactions: Chinese rhubarb alters fecal aromatic Amino acids and phenol metabolism – Shan Yin – Analytica Chimica Acta

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  • Microbes in the news

Stress may harm gut health as much as junk food – Honor Whiteman – Medical News Today

Different Microbial Communities Live Along Female Reproductive Tract – GenomeWeb

Gut Health May Begin in the Mouth – Lydialyle Gibson – Havard

October 20, 2017

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A wide variety of studies today from the digestive microbiota of carnivorous pitcher plants, to the skin microbiome of dogs, and the impacts of probiotics on male fertility in a mouse model of obesity. 

Events and jobs

Microbiome World Congress – November 7-8, 2017, Capital Hilton, Washington, DC – registration

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  • General microbiome

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae – Zhaobin Huang – Frontiers in Microbiology

Review: Uncultivated microbes in need of their own taxonomy – Konstantinos T Konstantinidis – The ISME Journal

Review: The growing tree of Archaea: new perspectives on their diversity, evolution and ecology – Panagiotis S Adam – The ISME Journal

  • Human respiratory microbiome

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition – Anton Y. Peleg – Journal of Cystic Fibrosis

  • Human gut microbiome

Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study – Thomas Howe McConville – PLOSone

Review: Antibiotics, gut microbiome, and obesity – Karen S. W. Leong – Clinical Endocrinology

Review: Gut microbiota changes in the extreme decades of human life: a focus on centenarians – Aurelia Santoro – Cellular and Molecular Life Sciences

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

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  • Animal Experiments

Lactobacillus rhamnosus PB01 (DSM 14870) supplementation affects markers of sperm kinematic parameters in a diet-induced obesity mice model – Fereshteh Dardmeh – PLOSone

  • Animal microbiome

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization – Beate M Slaby – The ISME Journal

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs – Andrew R. Williams – PLOSone

Individual signatures and environmental factors shape skin microbiota in healthy dogs – Anna Cuscó – Microbiome

Review: Metagenomic investigation of gastrointestinal microbiome in cattle – Minseok Kim – AJAS

  • Plant, root, and soil microbiome

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community – David W Armitage – The ISME Journal

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities – Roland C Wilhelm – The ISME Journal

Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness – David R. Toole – Biological Invasions

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis – Margarida M. Santana – Frontiers in Microbiology

  • Water and extremophile microbiome

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

Mixotrophy drives niche expansion of verrucomicrobial methanotrophs – Carlo R Carere – The ISME Journal

High abundance and expression of transposases in bacteria from the Baltic Sea – Theoden Vigil-Stenman – The ISME Journal

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB contaminated marine sediments – B. Matturro – FEMS Microbiology Ecology

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities – Oliver Röhl – Environmental Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept – Christina Pavloudi – PeerJ

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites – Gerrit Wienhausen – Frontiers in Microbiology

  • Built environment

Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome

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  • Probiotics / prebiotics

Review: Probiotics in the Prevention of Gestational Diabetes Mellitus – Luisa F. Gomez Arango – Nutrition and Diet in Maternal Diabetes

  • Phages and viruses

Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release – Gurinder K. Vinner – PLOSone

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology – Rachel L Marine – The ISME Journal

  • Techniques

A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping – Wan-Xiang Xu – PLOSone

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October 17, 2017

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The effects of antimicrobials in household products on the maternal and infant microbiome, water quality of an urban stream network, and using adaptive evolution to improve lager yeast hybrids.

Pregnancy and early life

Household triclosan and triclocarban effects on the infant and maternal microbiome – Jessica V Ribado – EMBO Molecular Medicine

Water and extremophile microbiome

Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations – L M Ward – Geobiology

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole – T L Hamilton – Geobiology

Built environment

Urban infrastructure influences dissolved organic matter quality and bacterial metabolism in an urban stream network – Clay P Arango – Freshwater Biology

Food microbiology

Pre-print: Enhanced wort fermentation with de novo lager hybrids adapted to high ethanol environments – Kristoffer Krogerus – bioRxiv

More microbes

Pre-print: Phosphate starvation induces replacement of phospholipids with the betaine lipid diacylglycerol-N,N,N-trimethylhomoserine in the human fungal pathogen Candida albicans – Surabhi Naik – bioRxiv

Microbes in the news

Infections by C.diff bacteria are on the rise and can cause serious problems – Consumer Reports – The Washington Post

Engineered bacteria build microstructures on their own – Michael Torrice – Chemical & Engineering News

Gut fungi might be linked to obesity and inflammatory bowel disorders – Tina Hesman Saey – Science News

Rare bacteria in dead elephant sparks alarm – Siba Mohanty – The New Indian Express

Woman Contracts Rare Bacterial Infection on 12-Hour Flight – Rachael Rettner – Live Science

Microbial Drug Resistant Mutations Found via Novel Genome Screen – Genetic Engineering and Biotechnology News

One More Small Piece of the Puzzle on the Role of Gut Micro-organisms in MS – Ana Belo Van Wijk – Multiple Sclerosis News Today

Microbes on the market

New Clinical Data and Microbiome Research from Rebiotix’s Phase 2 Program for RBX2660 Highlighted at the World Congress of Gastroenterology at ACG2017 – PR Newswire

October 11, 2017

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Events and jobs

Microbiology Laboratory Analyst – Cork (Ringaskiddy Road, Monkstown, Co. Cork)

 

Pregnancy and early life

Effect of probiotics on perinatal outcome in patients at high risk of preterm birth. – N Kirihara – The Journal of Obstetrics and Gynaecology Research

 

 

Human oral microbiome

Quantification of carious pathogens in the interdental microbiota of young caries-free adults. – D Bourgeois – PLoS One

 

Human gut microbiome

The gut microbiome in atherosclerotic cardiovascular disease – Z Jie – Nature Communications

Review: The microbiome as a novel paradigm in studying stress and mental health. – RT Liu – The American Psychologist

Review: The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – CL Hager – Digestive and Liver Disease

Review: Selected aspects of the human gut microbiota – M Ventura – Cellular and Molecular Life Sciences

 

Animal experiments 

Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. – C Ciu – PLoS One

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – X Qu – PLoS One

 

Animal microbiome 

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites – C Richards – PLoS One

 

Plant, root, and soil microbiome

The impact of the omics era on the knowledge and use of Lysobacter spp. to control phytopathogenic microorganisms. – G Puopolo – Journal of Applied Microbiology

The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores. – M Walter – Plant and Soil

Pathogenic potential of environmental resident fungi from ornithogenic soils of Antarctica – JRP Sousa – Fungal Biology

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh – DR Chaudhary – Microbial Ecology

 

Built environment 

Unravelling the core microbiome of biofilms in cooling tower systems. – L Di Gregorio – Biofouling

 

 

Phages and viruses

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics – S Roux – Nature Communications

Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – A Harms – bioRxiv

 

Techniques

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. – YW Yan – PLoS One

A GLM-based latent variable ordination method for microbiome samples. – MB Sohn – Biometrics

Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial – JM Pernica – PLoS One

A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast –  K Ishibashi – Scientific Reports

Analyses Approaches for Bacteria – E Ribeiro – Exposure to Microbiological Agents in Indoor and Occupational Environments

 

Microbes in the news

Bacteria self-organize to build working sensors – EurekAlert

Effects of nutritional factors on the intestinal microbiota – Freie Universität

October 7, 2017

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Events and jobs

Director of the Microbiome Research Laboratory – UT Southwestern

DOCTORAL STUDENT OR POSTDOCTORAL RESEARCHER –  Faculty of Veterinary Medicine, University of Helsinki – Application deadline: Nov 5, 2017

 

General microbiome

Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production – Y Boltyanskaya – Antonie van Leeuwenhoek

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. – MA Engevik – Microbiology Spectrum

 

Pregnancy and early life

Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father – LC Kenny – bioRxiv

 

Human respiratory microbiome

Long-term effects of inhaled corticosteroids on sputum bacterial and viral loads in COPD. – M Contoli – The European Respiratory Journal

 

 

Human gut microbiome

Bifidobacteria and the infant gut: an example of co-evolution and natural selection. – F Turroni – Cellular and Molecular Life Sciences

Inflammatory bactericidal lectin RegIIIβ: Friend or Foe for the host? – T Miki – Gut Microbes

Review: Host-microbiota interplay in mediating immune disorders. – KM Felix – Annals of the New York Academy of Sciences

Review: Probiotics for the prevention of Hirschsprung-associated enterocolitis: a systematic review and meta-analysis. – H Nakamura – Pediatric Surgery International

 

Animal experiments 

Can intestinal microbiota be associated with non-intestinal cancers? – C Jacqueline – Scientific Reports

Gnotobiotics: getting a grip on the microbiome boom – S Mallapaty – Lab Animal

Nanoparticle curcumin ameliorates experimental colitis via modulation of gut microbiota and induction of regulatory T cells. – M Ohno – PLoS One

 

Animal microbiome 

Comparative analysis of microbial communities associated with bacteriomes, reproductive organs and eggs of the cicada Subpsaltria yangi. – D Wang – Archives of Microbiology

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. – H Shen – Microbiology Open

Elucidating the microbial community associated with the protein preference of sludge degrading worms – S de Valk – Environmental Technology

 

Plant, root and soil microbiome

Mycorrhizal fungi show regular community compositions in natural ecosystems. – E Verbruggen – The ISME Journal

Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays – J Vacheron – Molecular Plant-Microbe Interactions

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development. – SC Castle – Oecologica

 

Water microbiome and extremophile 

Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. – D Kalenitchenko – The ISME Journal

Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages – BS  Park – Marine and Freshwater Research

Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. – R Rathour – Genome Announcements

 

Built environment 

Managing the excessive proliferation of glycogen accumulating organisms in industrial activated sludge by nitrogen supplementation: A FISH-NanoSIMS approach – CA Onetto – Systematic and Applied Microbiology

 

 

Phages and viruses

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. – G Freer – Current Medicinal Chemistry

 

Techniques

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing – P Schwendner – Microbiome

 

Microbes in the news

Puppies Linked To Bacterial Infection Outbreak Across 12 States – Forbes

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

Episode Review: VICE’s ‘Post-Truth News and Microbiome’ – The Hoya

Second grade handwashing experiment leads to big decrease in bacteria, illness – EurekAlert

Validating microbiome claims:Including the latest DNA techniques-Formulation Summit – Cosmetics Design Europe

Macromolecules: Weapons in the Fight Against Antibiotic Resistance  – American Veterinarian

Scientists are trying to figure out how to keep bacteria from running rampant on space missions – Popular Science

Bacteria can spread antibiotic resistance through soil – Phys.org

October 4, 2017

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Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

Elucidating the microbial community associated with the protein preference of sludge degrading worms – Steef de Valk – Environmental Technology

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass

 

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

October 1, 2017

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Events and jobs

Microbiome Center Networking Event – Plant Pathology and Environmental Microbiology, Penn State Agricultural College – October 3, 2017, 4:30 PM – 6:30 PM

General microbiome

Review: Old friends, microbes, and allergic diseases – N Shimojo – Allergology International

 

Human skin microbiome

Study of skin and nail Candida species as a normal flora based on age groups in healthy persons in Tehran-Iran – Z Rafat – Journal de Mycologie Médicale

 

Human gut microbiome

Variability in Eating Frequency is Associated with the Human Gastrointestinal Microbiota –  E Banishay – Journal of the Academy of Nutrition and Dietetics

Animal experiments 

The gut-liver axis: impact of a mouse model of small-bowel bacterial overgrowth –  Q Wang – Journal of Surgical Research

Metagenomic insights into the effects of oligosaccharides on the microbial composition of cecal contents in constipated mice – L Wang – Journal of Functional Foods

Effects of gut microbiota disturbance induced in early life on the expression of extrasynaptic GABA-A receptor α5 and δ subunits in the hippocampus of adult rat  – L Liang – Brain Research Bulletin

A Subset of Polysaccharide Capsules in the Human Symbiont Bacteroides thetaiotaomicron Promote Increased Competitive Fitness in the Mouse Gut – NT Porter – Cell and Host Microbe

Animal microbiome 

Hype or Opportunity? Using Microbial Symbionts in Novel Strategies for Insect Pest Control – AK Arora – Journal of Insect Physiology

Nutritional immunology: Diversification and diet-dependent expression of antimicrobial peptides in the black soldier fly Hermetia illucens – H Vogel – Developmental & Comparative Immunology

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – E Ruppé – Clinical Microbiology and Infection

Pathogen invasion changes the intestinal microbiota composition and induces innate immune responses in the zebrafish intestine – HT Yang – Fish & Shellfish Immunology

Plant, root and soil microbiome

Experimental warming reduces the diversity and functional potential of the Sphagnum microbiome – AA Carrell – bioRxiv

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome – S Jacquiod – Journal of Hazardous Materials

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms – M Wang – Ecotoxicology and Environmental Safety

Built environment 

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – CL Amorim – Ecotoxicology and Environmental Safety

Food microbiology

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

Review: Novel insights into the microbiology of fermented dairy foods – G Macori – Current Opinion in Biotechnology

Simulated gastrointestinal conditions increase adhesion ability of Lactobacillus paracasei strains isolated from kefir to Caco-2 cells and mucin – AA Bengoa – Food Research International

Chapter: Chapter 6 – Genetically Modified Microorganisms: Harmful or Helpful? – O Csutak – Genetically Engineered Foods

 

Techniques

Enhancement of subsoil denitrification using an electrode as an electron donor – S Qin – Soil Biology and Biochemistry

Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition – G Cesarano – Applied Soil Ecology

Next Generation Sequencing: Problems and opportunities for next generation studies of microbial communities in food and food industry – G Cardinali – Current Opinion in Food Science

An integrated electrolysis – electrospray – ionization antimicrobial platform using Engineered Water Nanostructures (EWNS) for food safety applications – N Vaze – Food Control

Inactivation of microbiota from urban wastewater by single and sequential electrocoagulation and electro-Fenton treatments – E Anfruns-Estrada – Water Research

Microbes in the news

I’ve always wondered: Why don’t hippos get cholera? – The Conversation

Women’s bacteria thwarted attempt at anti-HIV vaginal gel – Ottawa Citizen

How to Use Your Second Brain: Microbiome Expert Laure Ysebrant on Strategic Eating, Building Immunity, and Fake Fibre. – Thrive Global

A New Drug Uses CRISPR to Fight Antibiotic-Resistant Bacteria – Futurism

A TURNING OF PHAGE – Study Break

PEOPLE ARE MORE INTERESTING THAN BACTERIA: THE DR. CYRIL SHERER SAGA – The Jerusalem Post