Category Archives: Food Microbiology

October 30, 2017

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Today’s digest is short and sweet — including some articles on the connection between gut and bone metabolism, the biodegradation of oil in the ocean, and a good number of rhizosphere papers. Enjoy!

General Microbiome

Listeria monocytogenes virulence factors are secreted in biologically active Extracellular Vesicles – Carolina Coelho, bioRxiv

Multi-site human microbiome

Microbiota and cancer: a complex equation with a lot of exciting unknowns – Oxana Dmitrieva, Seminars in Immunology

Osteomicrobiology: A New Cross-Disciplinary Research Field – Claes Ohlsson, Calcified Tissue International

Prebiotics, Bone and Mineral Metabolism – Corrie M. Whisner, Calcified Tissue International

Human gut microbiome

Gut dysbiosis breaks immunological tolerance toward the central nervous system during young adulthood – Sudhir K. Yadav, PNAS

Clostridium difficile in Older Adults – Curtis J. Donskey, Infectious Disease Clinics of North America

The Microbiome That Shapes Us: Can It Cause Obesity? – Endashaw Omer, Current Gastroenterology Reports

Human oral microbiome

Infection’s Sweet Tooth: How Glycans Mediate Infection and Disease Susceptibility – Steven L. Taylor, Trends in Microbiology

Animal experiments

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs – Laura Glendinning, Microbiome

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome-from days to weeks – Bruno Tilocca, Microbiome

Hindgut mucosa-associated microbiome interacting with host regulating Escherichia coli O157:H7 shedding in cattle – Ou Wang, Applied and Environmental Microbiology

Plant, root, and soil microbiome

Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers – Hao Yu, Applied and Environmental Microbiology

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils – Alexandra Schwarz, Microbial Ecology

Identification of heterotrophic zinc mobilization processes among bacterial strains isolated from wheat rhizosphere (Triticum aestivum L) – Benjamin Costerousse, Applied and Environmental Microbiology

Seed defense biopriming with bacterial cyclodipeptides triggers immunity in cucumber and pepper – Geun Cheol Song, Scientific Reports

Characterization and potential of plant growth promoting rhizobacteria isolated from native Andean crops – Katty Ogata-Gutiérrez, World Journal of Microbiology and Biotechnology

Water and extremophiles microbiome

Biodegradation of dispersed oil in seawater is not inhibited by a commercial oil spill dispersant – Odd G. Brakstad, Marine Pollution Bulletin

Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent – Ke Wang, Bioresource Technology

Food microbiology

Yeast microbiota in artisanal cheeses from Corrientes, Argentina – Marina C. Cardozo, Revista Argentina de Microbiología

Flavonoids as detoxifying and pro-survival agents: What’s new? – Geir Bjørklund, Food and Chemical Toxicology

Techniques

Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces – Eliana P. Velásquez-Mejía, Applied Microbiology and Biotechnology

Microbes in the News

How a 672,000-Gallon Oil Spill Was Nearly Invisible – CHRISTINA CARON, New York Times

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 26, 2017

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In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

* Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

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 12, 2017

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Interesting papers from every category (especially in “Animal studies, animal microbiome”), and many on molecular mechanisms. Many of the alerts are from books (specifically on yeasts and soil/plant communities) listed below, so be sure to check their table of contents out!

Events and jobs
Biomedical Scientist – microbiology – Edinburgh, Scotland – Matchtech

Technician (Microbiology) – Birmingham, Alabama – LabCorp

Instructor in Microbiology – Corvallis, OR – Oregon State University

Senior Hospital Scientist Microbiology – Tamworth, New South Wales, Australia – NSW Health Pathology

Unlocking the Microbiome – November 15, London, UK – Microbiology Society

General microbiome
The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma – Microbial Ecology

Dysbiosis and Its Discontents – Katarzyna B. Hooks – mBio

Book: Yeasts in Natural Ecosystems: Ecology – Andrey Yurkov, María I. Pozo
Contains multiple articles of interest.

Pregnancy and early life
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment – Heidi Gumpert – Frontiers in Microbiology

Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy – Farzana Yasmin – Frontiers in Pediatrics

Multi-site human microbiome
Oral Lactobacillus Counts Predict Weight Gain Susceptibility: A 6-Year Follow-Up Study – J.A. Rosing – Obesity Facts

Review: Nutritional habits, risk, and progression of Parkinson disease – Roberto Erro – Journal of Neurology

Review: From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone – Emory Hsu – Calcified Tissue International

Human respiratory microbiome
Review: Role of microbiota on lung homeostasis and diseases – Jian Wang – Science China Life Sciences

Human gut microbiome
Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides – Kazune Tamura – Cell Reports

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence – Yunus E. Tuncil – mBio

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

Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes – Ophélie Rouxel – Nature Immunology

Review: How diet can impact gut microbiota to promote or endanger health – Benoit Chassaing – Current Opinion in Gastroenterology

Review: Management of inflammatory bowel disease-related anaemia and iron deficiency with specific reference to the role of intravenous iron in current practice – Jürgen Stein – Expert Opinion on Pharmacotherapy

Review: Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis – Wei Jia – Nature Reviews Gastroenterology and Hepatology

Review: Environmental triggers in IBD: a review of progress and evidence – Ashwin N. Ananthakrishnan – Nature Reviews Gastroenterology and Hepatology

Animal experiments
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch – PNAS

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine – Leore T. Geller – Science

Increased weight gain by C-section: Functional significance of the primordial microbiome – Keith A. Martinez II – Science Advances

Epicutaneous Tolerance Induction to a Bystander Antigen Abrogates Colitis and Ileitis in Mice – David Dunkin – Inflammatory Bowel Diseases

Dietary fatty acids control the species of N-acyl-phosphatidylethanolamines synthesized by therapeutically modified bacteria in the intestinal tract – Noura S Dosoky – ACS Infectious Diseases

In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis – Lorenna Machado – Microbial Ecology

Host effects on microbiota community assembly – Kathrin Näpflin – Journal of Animal Ecology
In bumblebees!

Animal microbiome
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia – Ashley Anne Ross – bioRxiv

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems
Drones were involved.

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function – Carolina Ramirez – Frontiers in Microbiology

A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis – Jie Yu – Frontiers in Microbiology

Amplicon sequencing of bacterial microbiota in abortion material from cattle – Sara Vidal – Veterinary Research

Plant, root, and soil microbiome
Book: Soil Biological Communities and Ecosystem Resilience – Editors Martin Lukac, Paola Grenni, Mauro Gamboni
Multiple articles of interest.

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – Eric R. Hester – bioRxiv

Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities – Xiaoyan Tian – Frontiers in Plant Science

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3 – Sumera Yasmin – Frontiers in Microbiology

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants – Dominik K Großkinsky – Experimental Botany

Gaining Insight into Plant Responses to Beneficial and Pathogenic Microorganisms Using Metabolomic and Transcriptomic Approaches – Fernando Matías Romero – Metabolic Engineering for Bioactive Compounds

Water and extremophile microbiome
Globally Important Haptophyte Algae Use Exogenous Pyrimidine Compounds More Efficiently than Thiamin – Magdalena A. Gutowskaa – mBio

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom – Jing-YunSun – Marine Environmental Research

Built environment
Biodegradation of tetracycline antibiotics in A/O moving-bed biofilm reactor systems – Han-Yu Chen – Bioprocess and Biosystems Engineering

Food microbiology
Interindividual Variability in Metabolism of [6]-Shogaol by Gut Microbiota – Pei Wang – Journal of Agricultural and Food Chemistry

Microbial technology
Programmed Assembly of Pressure Sensors Using Pattern-Forming Bacteria – Yangxiaolu Cao – Nature Biotechnology
Press: Three words: Synthetic gene circuit. Self-assembling bacteria build pressure sensor – Andrew Silver – The Register

Probiotics / prebiotics / antibiotics
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota – Richard Y. Wu – Microbiome

Review: Antibiotics and specialized metabolites from the human microbiota – Walaa K. Mousa – Natural Product Reports

Phages and viruses
Moderate-Throughput Identification and Comparison of Campylobacter-Infecting Bacteriophages – Tylor J. Johnson – bioRxiv

Review: Innate Viral Receptor Signaling Determines Type 1 Diabetes Onset – Zachary J. Morse – Frontiers in Endocrinology

Bioinformatics
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data – Masanori Kakuta – International Journal of Molecular Sciences

Microbes in the news
Hibernating ribosomes help bacteria survive – Saint Louis University – Science Daily
Paper: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus – Donna Matzov – Nature Communications

A century-old vaccine vial sheds light on one of medicine’s enduring mysteries – Helen Branswell – STAT News

Predatory bacteria-the quest for a new class of antibiotics – Phys.org

Mind the Gut: Copenhagen Exhibition Explores Bacteria and Feelings – Clara Rodríguez Fernández – Labiotech.eu

Gut Love: Bacteria, Love and Immunology Intersect at Esther Klein Gallery Exhibit – PRWeb

How mouldy mushrooms and frog spawn have been turned into art on Spring Bank – Amgus Young – Hull Daily Mail

Microbes on the market
Kaleido Biosciences and CoreBiome Partner to Accelerate Microbiome Therapeutic Development – Business Wire

Tiffany’s non-microbiology picks
The rise and fall and rise again of 23andMe – Erika Check Hayden – Nature

The future of DNA sequencing – Eric D. Green – Nature

October 9, 2017

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Events and jobs
Postdoctoral Researcher (Experimental or Computational) – Cornell University, Ithaca, NY

The Brito Lab at Cornell University in Ithaca, NY works in the area of systems biology of the human microbiome. We are looking for talented postdocs to fill two open positions for postdoctoral researchers interested in investigating mechanistic linkages between microbes and human health outcomes.

Postdoctoral candidates can have an experimental or computational background, or both. One of the positions will be focused on engineering—any experience with synthetic biology or biomaterials is a plus. There are a range of projects in the lab relating to: clinically relevant populations (i.e. inflammatory bowel and neutropenic patients); environmental transmission of organisms and antibiotic resistance; genetic engineering of bacteria; and international research related to the microbiome. The lab strives on the diverse backgrounds of students and postdocs (e.g. microbiology, biomedical engineering, computational biology and genetics).

Start dates are flexible, but could be as early as this Fall. Interested late-stage graduate students or recently-obtained PhDs, should send Ilana Brito (ibrito (at) cornell.edu) a cover letter and CV. Promising candidates will be invited for an interview. We offer a competitive salary and benefits package.

Pregnancy and early life
Diagnosis and management of diaper dermatitis in infants with emphasis on skin microbiota in the diaper area – Maja Šikić Pogačar – International Journal of Dermatology

Human respiratory microbiome
Upregulation of bacterial-specific Th1 and Th17 responses that are enriched in CXCR5+ CD4+ T cells in non-small cell lung cancer – Qin-Yun Ma – International Immunopharmacology

Human gut microbiome
Review: Microbiome-health interactions in older people – Paul W. O’Toole – Cellular and Molecular Life Sciences

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

Review: A comprehensive review of non-enterica subspecies of Salmonella enterica – Alexandre Lamas – Microbiological Research

Animal experiments
Effect of dietary supplements in American bullfrogs reared in low and high stocking densities – Jorgina Juliana Gradisse Freitas – Aquaculture Reports

Animal microbiome
Stenotrophomonas-like bacteria are widespread symbionts in cone snail venom ducts – Joshua P. Torres – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Microbial Resistance Mechanisms to the Antibiotic and Phytotoxin Fusaric Acid – Frankie K. Crutcher – Journal of Chemical Ecology

Book: Soil Pollution: From Monitoring to Remediation – Paula Alvarenga, Christian P. Andersen (editors)

Water and extremophile microbiome
Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics – Timothy Bush – Nature Communications

Built environment
Impact of carbon monoxide partial pressures on methanogenesis and medium chain fatty acids production during ethanol fermentation – Sofia Esquivel-Elizondo – Biotechnology and Bioengineering

Food microbiology
Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi – Clinical Gastroenterology and Hepatology

Tiny but mighty: bacterial membrane vesicles in food biotechnological applications – Yue Liu – Current Opinion in Biotechnology

10 – Microstructure, constituents, and their relationship with quality and functionality of dietary fibers – Naphaporn Chiewchan – Food Science, Technology and Nutrition

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li – Journal of Functional Foods

Probiotics / prebiotics
Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx – International Journal of Pharmaceutics

Review: Challenges and Opportunities of Nontraditional Approaches to Treating Bacterial Infections – Brian N Tse – Clinical Infectious Diseases

Probiotic intervention influences the salivary levels of Matrix Metalloproteinase (MMP)-9 and Tissue Inhibitor of metalloproteinases (TIMP)-1 in healthy adults – Heli Jäsberg – Archives of Oral Biology

Bioinformatics
Detection of complex structural variation from paired-end sequencing data – Joseph G. Arthur – bioRxiv

Codon-Dependent Translational Accuracy Controls Protein Quality in Escherichia coli but not in Saccharomyces cerevisiae – Lyne Jossé – bioRxiv

Techniques
A simple dilute and shoot approach incorporated with pentafluorophenyl (PFP) column based LC-MS/MS assay for the simultaneous determination of trimethylamine N-oxide and trimethylamine in spot urine samples with high throughput – Xiaoguang (Sunny) Li – Journal of Chromatography B

Microbes in the news
Multiple barriers to ending Madagascar’s plague outbreak – Andrew Masterson – Cosmos Magazine

A daughter’s affliction gives mother’s work ‘meaning and purpose’ – Liora Engel-Smith – The Sentinel

Antibiotic apocalypse’: doctors sound alarm over drug resistance – Robin McKie –
The Guardian

Want to cut your risk of urinary tract infection? Drink water, says study – Zee Media Bureau

Statins have power to help elderly fight off killer superbug – Sarah Westcott – Express

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

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

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

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

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

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 3, 2017

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Review on bioinformatics software for virus sequence analysis, the wild baboon microbiome, potential health risks of spontaneous food fermentation.

Human oral microbiome

Pre-print: Novel genes required for the fitness of Streptococcus pyogenes in human saliva – Luchang Zhu – bioRxiv

Human gut microbiome

Antibiotic use and new-onset inflammatory bowel disease in Olmsted County, Minnesota: a population-based case-control study – Satimai Aniwan – Journal of Crohn’s and Colitis

The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young – Gaorui Bian – mSphere

Animal experiments

Young Pigs Consuming Lysozyme Transgenic Goat Milk Are Protected from Clinical Symptoms of Enterotoxigenic Escherichia coli Infection – Lydia C Garas – The Journal of Nutrition

Whole-Grain Starch and Fiber Composition Modifies Ileal Flow of Nutrients and Nutrient Availability in the Hindgut, Shifting Fecal Microbial Profiles in Pigs – Janelle M Fouhse – The Journal of Nutrition

Lotus Seed Resistant Starch Regulates Gut Microbiota and Increases SCFAs Production and Mineral Absorption in Mice – Hongliang Zeng – Journal of Agricultural and Food Chemistry

Animal microbiome

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species – Emmanuel Guivier – Microbial Ecology

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons – Laura E Grieneisen – Integrative and Comparative Biology

Plant, root, and soil microbiome

Pre-print: Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium – Sarah Zecchin – bioRxiv

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie – George C Manning – Environmental Management

Pre-print: Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant – Dagmara Sirová – bioRxiv

Multitrophic interactions in the rhizosphere of a temperate forest tree affect plant carbon flow into the belowground food web – H R Maboreke – Soil Biology and Biochemistry

Water and extremophile microbiome

Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring – Lan Liu – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: Spontaneous Food Fermentations and Potential Risks for Human Health – Vittorio Capozzi – Fermentation

Phages and viruses

Review: Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” – Martin Hölzer – Advances in Virus Research

Bioinformatics

Nephele: A cloud platform for simplified, standardized, and reproducible microbiome data analysis – Nick Weber – Bioinformatics

More microbes

Pre-print: A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus – Abigail L Lind – bioRxiv

Pre-print: Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection – Gregory M LaMonte – bioRxiv

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