Category Archives: Transcriptomics Proteomics

July 6, 2017

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The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

April 5, 2017

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Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

March 11, 2017

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General microbiome

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – M Pammi – Microbiome

Is the 25 year hepatitis C marathon coming to an end to declare victory? – Khulood T Ahmed – bioRxiv

Natural antimicrobial peptide complexes in the fighting of antibiotic resistant biofilms: Calliphora vicina medicinal maggots – N Gordya – PLoS One

Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes – An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions – PM Swe – PLoS Neglected Tropical Disease

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – C Barthels – Nature Communications

Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal – I Khan – Medical Principles and Practice

 

Human skin microbiome

Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy

 

Human vaginal microbiome

*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology

 

Human gut microbiome

*Review: Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy – UC Ghoshal – Gut and Liver

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – H Tilg – Cell Metabolism

Melatonin prevents obesity through modulation of gut microbiota in mice – P Xu – Journal of Pineal Research

 

Animal microbiome

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats – Vientós-Plotts AI – PLoS One

A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – R Batacan – Journal of Applied Microbiology

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – MS Llewellyn – Scientific Reports

Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile, haemato-biochemical parameters and immune responses – A Nandi – Aquaculture Research

 

Plant, root and soil microbiome

Simplified and representative bacterial community of maize roots – B Niu – PNAS

Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba) – R Prior – Journal of Environmental Science and Health, Part B

Thermophilic microorganisms in arable land around medieval archaeological sites in Northern Caucasus, Russia: Novel evidence of past manuring practices – E Chernysheva – Geoarchaeology

 

Water and Extremophiles

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – AR Rowe – Environmental Microbiology

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – M Kwon – Environmental Microbiology

 

Transcriptomics and Proteomics

A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv

 

Techniques

Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis – L D’Amico – Lab on a Chip

A fast small-sample kernel independence test for microbiome community-level association analysis – X Zhan – Biometrics

 

More microbes

Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health – Leulier F – Cell Metabolism

Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa – EM Waters – Thorax

*Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Meibomian gland disease and the microbiotome: is it time for ocular probiotics? – S Watson – Clinical & Experimental Ophthalmology

*Review: Infection in Organ Transplantation – JA Fishman – American Journal of Transplantation

Azole resistance in Candida albicans from animals: Highlights on efflux pump activity and gene overexpression – MFG Rocha – Mycoses

The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae) – F Gomez – Journal of Eukaryotic Microbiology

Gut microbiota analysis in rats with methamphetamine-induced conditioned place preference – T Ning – bioRxiv

 

Microbes in news

What is Metagenomics? – Y Smith – News Medical

UCC researchers discover weapon to fight antibiotic resistance – D Ahlstrom – The Irish Times

Community gets an eye-opening lesson in human microbiome and our western lifestyle – C MacDonald – UToday

Microbiome Research Symposia Review: Microbiome and Diseases – J Phelan – Taconic Biosciences

Q&A with Zeus Capital’s Dr Gary Waanders: Live Biotherapeutics & 4D Pharma PLC (LON:DDDD) – A Stone – Directors Talk Interviews

Do You Have the Guts to Perform? Microbial Balance, the Brain and Athletic Performance – SJ Hewlings – Natural Products Insider

New probiotics meant to balance microbial, fungal communities in gut – H Schultz – NUTRAingredients

Google Leads $51M Investment in Startup Tackling Drug-Resistant Bacteria – R Bushey – R & D

Your bacteria-ridden makeup could be the reason you keep getting sick – A Mulvaney – Independent

February 25, 2017

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Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

January 14, 2017

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So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

January 7, 2017

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3D modeling of endometrial interaction with vaginal bacteria, insect symbiont determined by host plants, 2011 tsunami effects on  phytoplankton, virus taxonomy, Microbiome Helper and microRNA sensitivity in intestinal stem cells.

Human vaginal microbiome

* Human three-dimensional endometrial epithelial cell model to study host interactions with vaginal bacteria and Neisseria gonorrhoeae – Paweł Łaniewski – Infection and Immunity

Human gut microbiome

Workshop Proceedings: Nutrition Across the Lifespan for Healthy Aging – Proceedings of a Workshop—in Brief – NAS

Review: Gut–brain axis in 2016: Brain–gut–microbiota axis — mood, metabolism and behaviour – Timothy G. Dinan & John F. Cryan – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age – Gangsik Han – Microbial Ecology

Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs – Kait Al – PeerJ

* Host plant species determines symbiotic bacterial community mediating suppression of plant defenses – Seung Ho Chung – Scientific Reports

Animal microbiome

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges – Gerald Lackner – PNAS

Plant, root, and soil microbiome

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria – Jana Klikno – Protoplasma

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices – Yong Tan – Journal of Basic Microbiology

Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade – Alexander P. Petroff – Journal of Statistical Physics

Water microbiome

* Retrospective analysis of phytoplankton assemblages on the Iwate coast before and after the 2011 tsunami using cryopreserved DNA samples – Yutaka Okumura

Effects of iron deficiency on the growth and photosynthesis of three bloom-forming cyanobacterial species isolated from Lake Taihu – Kui Xu – Phycological Research

Patterns of bacterial diversity in the marine planktonic particulate matter continuum –
Mireia Mestre – The ISME Journal

Bioreactor, waste, and pollution microbiology

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Accelerated acidification by inoculation with a microbial consortia in a complex open environment – Jiadong Yu – Bioresource Technology

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community – Jin-tian Li – Plant and Soil

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants? – A. Miłobędzka – Water Science & Technology

Frequency dependent microbial growth during cycles of feast and famine – Jason Merritt – arXiv

Viruses and phages

* Consensus statement: Virus taxonomy in the age of metagenomics – Peter Simmonds – Nature Reviews Microbiology

Genomic evolution of bacterial populations under coselection by antibiotics and phage
– Johannes Cairns – Molecular Ecology

Bioinformatics and metagenomics

* Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems

Transcriptomics

* Functional transcriptomics in diverse intestinal epithelial cell types reveals robust microRNA sensitivity in intestinal stem cells to microbial status – Bailey C.E. Peck – Journal of Biological Chemistry

Biofilms

Tackling Fungal Resistance by Biofilm Inhibitors – Shanchao Wu – Journal of Medical Chemistry

Microbes in the news

Featuring our research: The Secret Lives of Marine Mammal Microbes – Probing the mystery of what goes on inside the guts of dolphins and whales – Emma Hiolski – Scientific American

That cold you have might actually be the worst Bay Area flu outbreak in a decade – Kristin Hanes – SF Gate

Microbiomes in far-flung places: characterizing the arctic Inuit gut microbiome – Stephen Ornes – ASM

Microbes on the market

MoBio’s Microbiome News is back!

OptiBiotix Release: Microbiome Technology Powers The Healthy Weight Loss Company Expansion – BioSpace

Bik’s Non-Microbiology Picks

The crack in this Antarctic ice shelf just grew by 11 miles. A dramatic break could be imminent – Chris Mooney – Washington Post

Citizen Science: It’s that time of year: the annual bird count – Shawn Price – Los Angeles Times

December 31, 2016

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Human lung microbiome

Study of the Lung Microbiome. Have We Reached the End of the Beginning?  – Alison Morris – American Journal of Respiratory and Critical Care Medicine

Microbes at nearly sterile sites

The Clinical Impact of Rapid, Direct MALDI-ToF Identification of Bacteria from Positive Blood Cultures – Kathryn French – PLOS ONE

Animal experiments

Impacts of resistant starch and wheat bran consumption on enteric inflammation in relation to colonic bacterial community structures and short-chain fatty acid concentrations in mice – Janelle A. Jiminez – Gut Pathogens

Animal microbiome

A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance – Jeffery K. Tomberlin – Annals of the Entomological Society of America

Comparative community structure of archaea in rumen of buffaloes and cattle – Shyam S Paul – Journal of the Science of Food and Agriculture

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest – Martin Hartmann – Molecular Ecology

Water and extremophile microbiome

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor – Chang-Hong Liu – Environmental Microbiology

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes – Vittorio Boscaro – Microbial Ecology

Microbial diversity and autotrophic activity in Kamchatka hot springs – Alexander Yu – Extremophiles

Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities – Michelle A. Berry – Environmental Microbiology

Built environment microbiome

An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air

Sandpits as a reservoir of potentially pathogenic fungi for children – Anna Wójcik – Ann Agric Environ Med

Food microbiome

Microbiological characterization of vegetables and their rhizosphere soil in Eastern Poland – Teresa Kłapeć – Ann Agric Environ Med

Proteomics

Comparing genome versus proteome-based identification of clinical bacterial isolates
Valentina Galata – Briefings Bioinformatics

Microbes in the news

Now Sixty food poisoning cases ‘from farm’s trendy raw milk’ leads a judge to slap a ban on the business to block them from selling any more – Liz Hull – The Daily Mail

The Changing Face of American Forests. How pollution deposes dominant tree species and releases soil carbon – Nala Rogers – Inside Science

Can Bacteria Help Stop the Spread of Disease? – Infection Control Today

How Do Multidrug-Resistant Bacteria Survive Antibiotics Without Resistance Genes? – Contagion LIve

Easy, crunchy, healthy sauerkraut – Cindy Grace – AJC

Science, publishing, and career

Who Believes in the Storybook Image of the Scientist? – Coosje L. S. Veldkamp – Accountability in Research

What Scientists Think About Scientists – Neuroskeptic – Discover

November 24, 2016

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Happy Thanksgiving! My inbox was full of exciting new papers, so here is a digest before I start cooking.

Microbiota and epigenetics, predatory bacteria to control infection, bacteria control water levels in leaves, microbial volatile compounds affect plant growth, the invertebrate virome, and natural products as mediators of disease.

Human respiratory microbiome

Evidence of microbiota dysbiosis in chronic rhinosinusitis – Michael Hoggard – International Journal of Allergy & Rhinology

Human gut microbiome

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins – Emily R. Davenport – BMC Genomics

New treatment options for irritable bowel syndrome with predominant diarrhea – Weber, H. Christian – Current Opinion in Endocrinology, Diabetes and Obesity

Animal models

* Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues – Kimberly A. Krautkramer – Molecular Cell

Press: Changes in the diet affect epigenetics via the microbiota – EurekAlert
Gut’s microbial community shown to influence host gene expression – EurekAlert

* Injections of Predatory Bacteria Work Alongside Host Immune Cells to Treat Shigella Infection in Zebrafish Larvae – Alexandra R. Willis – Current Biology

Harnessing the power of predatory bacteria as a ‘living antibiotic’ – Phys.org

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice – Tze Guan Tan – PNAS

Plant, root, and soil microbiome

+ Bacteria establish an aqueous living space in plants crucial for virulence – Xiu-Fang Xin – Nature

Press: Bacteria Spread Infection in Plants by Manipulating Water Level in Leaves – Howard Hughes Medical Institute

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus – Jonathan W. Leff – New Phytologist

Host species and environmental variation can influence rhizobial community composition
– Holly B. Vuong – Journal of Ecology

* Arabidopsis Responds to Alternaria alternata Volatiles by Triggering Plastid Phosphoglucose Isomerase-Independent Mechanisms – Ángela María Sánchez-López – Plant Physiology
* Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action – Ángela María Sánchez-López – Plant, Cell & Environment
* Commentary: The methylerythritol 4-phosphate pathway as a metabolic crossroad for microbial and plant volatile organic compounds – Manuel Rodriguez-Concepcion – Plant, Cell & Environment

Press: Compounds produced by phytopathogenic microbes encourage plant growth – EurekAlert

Water and extremophile microbiome

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers – Maggie C. Y. Lau – PNAS

Viruses and phages

* Redefining the invertebrate RNA virosphere – Mang Shi – Nature

World of viruses uncovered. Pioneering study of invertebrates discovers 1,445 viruses including several new families – EurekAlert

Metabolomics

* Review: Natural products as mediators of disease – Neha Garg – Natural Products Reports

Techniques

Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe – Sena Bae – PNAS

Research highlight: Culturomics: illuminating microbial dark matter – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Microbes in the news

Small world: The hot field of the microbiome. Ever since the discovery that bacteria can be good for us, there’s been a race to get into the lab. With Christine Szymanski and Josh Neufeld – Sharon Oosthoek – Maclean’s

Allergies: D-tryptophan explains probiotic characteristics of bacteria – Health Canal

Bacteria-destroying robot could replace antibiotics: Dutch inventer (sic) – Janene Pieters – NLTimes

Molecular chameleons reveal bacterial biofilm – EurekAlert

QIAGEN and CosmosID Launch New Plugin for Metagenomics Analysis – BusinessWire

Milliken recalls carpet cleaning powder on bacteria fears – Reuters

Bik’s non-microbiology Picks

Influence of Pokémon Go on Physical Activity: Study and Implications – Tim Althoff – arXiv

Aspartame may prevent, not promote, weight loss by blocking intestinal enzyme’s activity – EurekAlert

November 21, 2016

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Why is the human vaginal microbiome unique, multiple sclerosis, fiber-deprived gut microbes eating mucus, vertical structure of the phyllospere, cave microbiome, resistome.

Pregnancy and early life

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study – Kaori Tachibana – Journal of Diabetes Investigation

Human vaginal microbiome

Lactobacilli Dominance and Vaginal pH: Why is the Human Vaginal Microbiome Unique? – Elizabeth A. Miller – Frontiers in Microbiology

Human gut microbiome

Prevalence of Small Intestinal Bacterial Overgrowth in Multiple Sclerosis: a Case-Control Study from China – Yongbo Zhang – Journal of Neuroimmunology

MyNewGut: Insulin resistance as key factor for linking modulation of gut microbiome to health claims and dietary recommendations to tackle obesity – Stoffer Loman -Trends in Food Science & Technology

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Review: Microbiome and nutrition in autism spectrum disorder: current knowledge and research needs – Kirsten Berding – Nutrition Reviews

Review: Th Role of Short-Chain Fatty Acids in Kidney Injury Induced by Gut-derived Inflammatory Response – Wei Huang – Metabolism

Review: Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition – Keerati Wanchai – The American Journal of the Medical Sciences

Animal and in vitro experiments

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility – Mahesh S. Desai – Cell
Editorial: Veggies and Intact Grains a Day Keep the Pathogens Away – Francesca S. Gazzaniga – Cell
Press: High-fiber diet keeps gut microbes from eating the colon’s lining, protects against infection, animal study shows – Science Daily

Coevolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection – Suzanne A. Ford – Molecular Ecology

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection – Yixin H. Ye – Journal of Invertebrate Pathology

Modulation of the cytokine profile in Caco-2 cells by faecal lactobacilli and bifidobacteria from individuals with distinct dietary habits – Diomira Luongo – Cytokine

An Alteration in the Cecal Microbiota Composition by Feeding of 1-Kestose Results in a Marked Increase in the Cecal Butyrate Content in Rats – Takumi Tochio – PLOS ONE

Animal microbiome

Proteome data on the microbial microbiome of grasshopper feces – Nico Jehmlich – Data in Brief

Plant, root, and soil microbiome

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing – Ayako Izuno – PLOS ONE

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities – Rafal Zgadzaj – PNAS

Press: Nitrogen-fixing symbiosis is crucial for legume plant microbiome assembly – EurekAlert

Influence of salt tolerant Trichoderma spp. on growth of maize (Zea mays) under different salinity conditions – Krishna Kumar – Journal of Basic Microbiology

Review: Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review – Abdelaal Shamseldin – Symbiosis

Review: Forest microbiome: diversity, complexity and dynamics – Petr Baldrian – FEMS Microbiology Reviews

Review: The cave microbiome as a source for drug discovery: reality or pipe dream? – Soumya Ghosh – Biochemical Pharmacology

Extremophile microbiome

Opinion: Colonization of Black Smokers by Hyperthermophilic Microorganisms – Reinhard Wirth – Trends in Microbiology

Food microbiology

Biofilms formed by microbiota recovered from fresh produce: Bacterial biodiversity, and inactivation by benzalkonium chloride and enterocin AS-48 – Mª José Grande Burgos – LWT – Food Science and Technology

Metabolomics

Comparative in silico analysis of butyrate production pathways in gut commensals and pathogens – Swadha Anand – Frontiers in Microbiology

Resistome

Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria – Sabrina Duranti – Applied and Environmental Microbiology

Review: Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
– José L. Martínez – Annals of the New York Academy of Sciences

Microbes in the news

I got my gut sequenced – and found out I need to go to the dentist – Liam Mannix – Sydney Morning Herald

Bighorn sheep transfer OK’d despite concerns about disease – Brett French – Missoulian
http://missoulian.com/news/state-and-regional/bighorn-sheep-transfer-ok-d-despite-

High-Fat Diets Alter Gut Microbiota, Leading to Increased Choroidal Neovascularization – Dava Stewart – HCP Live

Student scientists engineer bacteria to break down plastic, hope to help clean Baltimore harbor – Scott Dance – The Baltimore Sun

Soil bacteria helps protect rice plants from arsenic and fungus. ‘Cocktail’ of soil bacteria can protect rice plants from deadly forces – Science Daily
Bacteria Might Be Able To Help Rice Affected By Fungus – Rodney Rafols – iTechPost

November 15, 2016

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Microbial profiling in the classroom, viral abundance in seawater membrane vesicles, two Akkermansia in vitro studies, the phyllospere of Phoenix’ urban forest, the (im)possibility to reconstruct plasmids, high confidence protein annotations.

General microbiome

Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont – Lynn Chiu – PhilSci Archive

Microbial Community-Level Physiological Profiling as an Inquiry Laboratory Exercise – Pamela A. Marshall – The American Biology Teacher

Human oral microbiome

Bacterial communities associated with apical periodontitis and dental implant failure – Simon Dingsdag – Microbial Ecology in Health and Disease

Human respiratory microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff –  Current Opinion in Pulmonary Medicine

Human gut microbiome

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh – Shafiqul Alam Sarker – Environmental Microbiology

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery – Priscila Sala – Journal of International Medical Research

Review: The Human Microbiome and I-Cubed: A Modern Medical Paradigm – David S. Younger – World Journal of Neuroscience

Animal and in vitro models

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent – F. Van Herreweghen – Beneficial Microbes

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism – Renee L. Greer – Nature Communications

Animal microbiome

Black rhinoceros (Diceros bicornis) and domestic horse (Equus caballus) hindgut microflora demonstrate similar fermentation responses to grape seed extract supplementation in vitro – N. F. Huntley – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Zhongmin Dai – Scientific Reports

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University

Diversity of phylloplane microflora in certain tea cultivars of Assam, North-East India – Amarjyoti Tanti – European Journal of Biological Research

Review: Do genetically modified plants affect adversely on soil microbial communities?
– Zheng-jun Guan – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology

Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches – Valerie F. Schwab – Biogeosciences

Trade-off between taxon diversity and functional diversity in European lake ecosystems – Lars Grossmann – Molecular Ecology

Glycerol enhances fungal germination at the water-activity limit for life – Andrew Stevenson – Environmental Microbiology

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India – Amrita Kumari Panda – AMB Express

Phages and viruses

Next-generation sequencing and norovirus – Matthew Cotten & Marion Koopmans – Future Virology

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates – Steven J Biller – ISME Journal

Metagenomics and bioinformatics

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data – Sergio Arredondo-Alonso – bioRxiv

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Optimal prediction of the number of unseen species – Alon Orlitsky – PNAS

Constraint-based stoichiometric modelling from single organisms to microbial communities
– Willi Gottstein – Journal of the Royal Society Interface

Metabolomics, culturomics, proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns – Emma Timmins-Schiffman – The ISME Journal

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols – Max Crüsemann – Journal of Natural Products

Probiotics

Review: Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis – Jennifer McKean – The Journal of Alternative and Complementary Medicine

Microbes in the news

Good News at Fred Hutch: Evolutionary biologists Drs. Harmit Malik and Jesse Bloom win American Society for Microbiology awards – Fred Hutch

NTU don once downed a dish of live bacteria, for science’s sake – Straits Times

MCR-1 resistance gene could make its way into bacteria and superbugs in Australia – NT News
Biofilm battle is key to antibiotic war – University of Queensland

‘Probiotics’ on salad greens could make them safer, healthier – The University of Queensland

Monique Keiran: Laziness and hubris making us sick – Times Colonist

From the American Heart Association annual meeting: Could C-Section Birth Raise Child’s Risk of Obesity? – Dennis Thompson – Pantagraph