Category Archives: Animal experiments

July 5, 2017

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General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

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

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

June 30, 2017

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A few gut microbiome reviews, apparently a simple bacterial community in bullet ants, circadian rhythm of rhizosphere bacterial communities, and you might want to think twice before you step into the ocean for a swim this summer.

General microbiology

Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities – Tahir Yusufaly & James Q. Boedicker – ePub in Physical Biology, first in arXiv

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber, R Fredrik Inglis and Rolf Kümmerli – ISME Journal

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas – Rosaria Campilongo et al. – PLoS Genetics

PrePrint: Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli – Johan H. van Heerden et al. – bioRxiv

Performance of electro-spun carbon nanofiber electrodes with conductive poly(3,4-ethylenedioxythiophene) coatings in bioelectrochemical systems – Juan J.L. Guzmana & Meryem O. Pehlivaner Kara et al. – Journal of Power Sources

Press: Bacteria-coated nanofiber electrodes digest pollutants – Blaine Friedlander – Phys.org

Human skin microbiome

Review: Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin – Katharina Bitschar et al. – Journal of Dermatological Science

Human gut microbiome

Review: The nutrition-gut microbiome-physiology axis and allergic diseases – Craig McKenzie – Immunological Reviews

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease – Ashton JJ et al. – Medicine (Baltimore)

Review: The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology – Nathan T. Porter and Eric C. Martens – Annual Reviews of Microbiology

Review: Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy – Rosita Aitoro et al. – Nutrients

Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients – Qing He & Yuan Gao et al. – GigaScience

Animal experiments

PrePrint: Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes – Matthew L Jenior et al. – bioRxiv

Animal microbiome

PrePrint: Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology – Ashley L. Marcinkiewicz et al. – bioRxiv

Diversity and Persistence of the Gut Microbiome of the Giant Neotropical Bullet Ant – Corrie S. Moreau & Benjamin E. R. Rubin – Integrative and Comparative Biology

PrePrint: Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang & Daniel Rozen – bioRxiv

Plant, root and soil microbiome

Effects of habitat constraints on soil microbial community function – Naoise Nunan et al. – Scientific Reports

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism – Christopher Staley et al. – Microbiome

Biological control of Pythium, Rhizoctonia and Sclerotinia in lettuce: the plant protective activity of the bacterium Paenibacillus alvei K165 is associated with the induction of systemic resistance – G. Fatouros et al. – Plant Pathology

Water and extremophile microbiome

Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome – Gerald K. Matar & Samik Bagchi et al. – Water Research

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo et al. – Journal of Microbiological Methods

Built environment

Hospital Building and Healthcare Associated Infections (HAIs) in terms of total contamination data and cases grouped by department/areas – Shadha M. Abbas Al Asadi – Scientific Journal of Medical Research

Microbes in the news

The Bugs That Keep Us Safe – Maria-Luisa Alegre – American Journal of Transplantation

Study on human skin microbiome finds archaea abundance associated with age – Phys.org

The Dust Storm Microbiome – Weismann Institute of Science – Laboratory Equipment

Starbucks’ iced coffee may have fecal bacteria in it — so do all these other things – Donovan Harrell – Miami Herald (BBC investigation)

Bacteria change a liquid’s properties and escape entrapment – Gail Mccormick – Phys.org

Only association: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows – DailyMail

Elevated bacteria counts found at 4 Island beaches – Rick Kelley – Valley Morning Star

Plasmids: traffickers of antibiotic resistance – Modernising Medical Microbiology – University of Oxford

Microbes on the market

Diabetes: J&J and Seventure Partners launch investment – tg – European Biotechnology

Global Microbiome Drugs Market 2017- Pfizer, Second Genome , Seres Therapeutics, MaaT Pharma, Enterome Bioscience – Nakul Shirke – Daily Hover

June 28, 2017

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Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE

June 24, 2017

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An early life focus today: Interesting papers on the effects of a pre-term cesarian birth on the gut microbiome and the impact of the infant gut microbiome on food allergies. Also highlighted, the relationship between the gut microbiome and social stress vulnerability in mice, the role of the gut microbiome in mosquito development, and evidence of a permanent transfer of prokaryotic virus sequences to the mammalian brain.

  • Pregnancy and early life

Review: Perinatal Group B Streptococcal Infections: Virulence Factors, Immunity, and Prevention Strategies – Jay Vornhagen – Trends in Microbiology

* Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants – Christopher Stewart – Frontiers in Microbiology

* A prospective microbiome-wide association study of food sensitization and food allergy in early childhood – Jessica Savage – Allergy

  • Human respiratory microbiome

Psl Produced by Mucoid Pseudomonas aeruginosa Contributes to the Establishment of Biofilms and Immune Evasion – Christopher Jones – mBio

  • Human skin microbiome

Isotretinoin and lymecycline treatments modify the skin microbiota in acne – Hanna-Lenna Kelhala – Experimental Dermatology

  • Human oral microbiome

Potassium is a key signal in host-microbiome dysbiosis in periodontitis – Susan Yost – PLOS Pathogens

  • Human gut microbiome

The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue – Rebecca Schugar – Cell Reports
In vitro modulation of gut microbiota by whey protein to preserve intestinal health – Sanchez-Moya – Food and Function

Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis – Gregory Young – Frontiers in Cellular and Infection Microbiology

NOD2 genetic variants predispose one of two familial adenomatous polyposis siblings to pouchitis through microbiome dysbiosis – Kathleen Schieffer – Journal of Crohn’s and Colitis

The Bacteroides fragilis pathogenicity island links virulence and strain competition – Benjamin Casterline – Gut Microbes

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients – Jihan Wang – PeerJ

Gut microbiota of liver transplantation recipients – Li-Ying Sun – Scientific Reports

Review: Microbiome: A Potential Component in the Origin of Mental Disorders – George Stefano – Medical Science Monitor

Review: Impact of mycotoxins on the intestine: are mucus and microbiota new targets? – Herve Robert – Journal of Toxicology and Environmental Health

Review: Microbiota, Inflammation and Colorectal Cancer – Cecily Lucas – International Journal of Molecular Sciences

Review: The Enteric Network: Interactions between the Immune and Nervous Systems of the Gut – Bryan Yoo – Immunity

  • Cadaver microbiome

Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition – Javier Pascual – Environmental Microbiology

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  • Animal experiments

* Implications of the gut microbiota in vulnerability to the social avoidance effects of chronic social defeat in male mice – Joanna Kasia Szyszkowicz – Brain, Behavior, and Immunity

Intestinal microbial dysbiosis aggravates the progression of Alzheimer’s disease in Drosophila – Shih-Cheng Wu – Nature Communications

Fructo-oligosaccharides and intestinal barrier function in a methionine-choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS One

Spirulina Protects against Hepatic Inflammation in Aging: An Effect Related to the Modulation of the Gut Microbiota? – Audrey Neyrinck – Nutrients

Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice – C.J Chang – International Journal of Obesity

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors – Adam SanMiguel – Antimicrobial Agents and Chemotherapy

Temporal microbiota changes of high-protein diet intake in a rat model – Chunlong Mu – Anaerobe

  • Animal microbiome

Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2 – Guowei Zhou – Environmental Microbiology

Effects of dietary supplementation of red pepper (Schinus terebinthifolius Raddi) essential oil on performance, small intestinal morphology and microbial counts of weanling pigs – Pedro Leon Gomes Cairo – Science of Food and Agriculture

Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen – Kelly Barnhart – Microbial Ecology

* Bacteria-mediated hypoxia functions as a signal for mosquito development – Kerri Coon – PNAS

  • Plant, root, and soil microbiome

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation – Eduardo de Siva Fonseca – Microbial Ecology

  • Water and extremophile microbiome

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses – Vera Thiel – Frontiers in Microbiology

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  • Phages and viruses

* A prokaryotic viral sequence is expressed and conserved in mammalian brain – Yang-Hui Yeh – PNAS

  • Techniques

Solid Sampling with a Diode Laser for Portable Ambient Mass Spectrometry – Yeni Yung – Analytical Chemistry

June 22, 2017

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Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 16, 2017

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Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  

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  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology

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  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology

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  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv

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  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of Microbes – Kyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI

June 15, 2017

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Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

June 13, 2017

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Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 10, 2017

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Jobs and events

Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota

Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM

 

General microbiome

Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics

Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology

Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology

 

Human gut microbiome

Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model –  N Yin – Chemosphere

Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review

 

Animal experiment

A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy

 

Animal microbiome

Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development

 

Plant, root and soil microbiome

The nodule microbiome; N2-fixing rhizobia do not live alone  – P  Martínez-Hidalgo – Phytobiomes Journal

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology

Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry

Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology

 

Water microbiome and extremophile

Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica

Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research

 

Techniques

Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv

Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy

 

Metabolomics

Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla –  F Gu – AMB Express

 

Phages

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics

 

Built environment microbiome

Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv

Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research

 

More microbes

Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses

Protozoa and microbiome  – SL Burgess – Infection and Immunity

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens  – JE Heindl – bioRxiv

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv

 

Microbes in news

Engineering ‘good’ bacteria to kill bad ones – The Straits Times

White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos

Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire

New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism

Therapy could stop superbugs on farms – P Ghosh – BBC News

SHU students travel to present phages research – P Parise – Setonian Online

June 9, 2017

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Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today