September 21, 2017

Additional data and new analyses from the NIH Human Microbiome Project, understanding lambda phage integration in its effects on the host, a yeast fermentation method for use in wine making.

Pregnancy and early life

Pre-print: Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing – Anuradha Ravi – bioRxiv

Multi-site human microbiome

Strains, functions and dynamics in the expanded Human Microbiome Project – Jason Lloyd-Price – Nature

Phages and viruses

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology – Yu Tanouchi – mBio

Techniques

The 16S rRNA gene-based PCR method used for the detection of segmented filamentous bacteria in the intestinal microbiota generates false-positive results – Forough L Nowrouzian – Acta Pathologica, Microbiologica, et Immunologica Scandinavica

Pre-print: Wine yeast phenomics: a standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions – Emilien Peltier – bioRxiv

More microbes

Pre-print: Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – Corey S Westfall – bioRxiv

Microbes in the news

What’s the latest on gut microbiota? Concordia microbiology undergrads publish their findings – Phys.Org

Microbes on the market

Ixcela Launches Over-the-Counter Gut Health Test and Sophisticated Internal Wellness Program – Business Wire

Avadim Technologies Inc. Announces Partnership With Cardinal Health, Inc. – Market Wired

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September 4, 2017

Interaction of gut microbiota metabolites with host chromatin, modulation of T cell responses by Propionibacterium acnes in healthy and diseased skin, metatranscriptomics of the termite gut microbiota.

Multi-site human microbiome

Review: The potential of the microbiota to influence vaccine responses – David J Lynn – Journal of Leukocyte Biology

Human skin microbiome

Phenotype and antimicrobial activity of Th17 cells induced by Propionibacterium acnes strains associated with healthy and acne skin – George W Agak – Journal of Investigative Dermatology

Human gut microbiome

Review: The intricate connection between diet, microbiota, and cancer: A jigsaw puzzle – Melek Canan Arkan – Seminars in Immunology

Animal experiments

Characterization of vaginal microbiota of endometritis and healthy sows using high-throughput pyrosequencing of 16S rRNA gene – Jun Wang – Microbial Pathogenesis

Paneth Cell Defects Induce Microbiota Dysbiosis In Mice And Promote Visceral Hypersensitivity – Ambre Riba – Gastroenterology

Novel Interactions between Gut Microbiome and Host Drug-processing Genes Modify the Hepatic Metabolism of the Environmental Chemicals PBDEs – Cindy Yanfei Li – Drug Metabolism and Disposition

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa) – Qianqian Huang – Archives of Microbiology

Effect of dietary copper level on the gut microbiota and its correlation with serum inflammatory cytokines in Sprague-Dawley rats – Feng Zhang – Journal of Microbiology

Animal microbiome

Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome – Martyna Marynowska – BMC Genomics

Plant, root, and soil microbiome

Review: Wetland management using microbial indicators – Hidetoshi Urakawa – Ecological Engineering

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria are Small and Depend on Glyphosate-Use History – Daniel C Schlatter – Applied and Environmental Microbiology

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest – Can Du – Journal of Microbiology

Water and extremophile microbiome

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters – Zhen-Chao Zhou – Environmental Science and Pollution Research

Probiotics/prebiotics

Intestinal Microbiota in Infants at High-risk for Allergy: Effects of Prebiotics and Role in Eczema Development – Harm Wopereis – Journal of Allergy and Clinical Immunology

Metabolomics

Review: Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin – Kimberly A Krautkramer – Translational Research

Microbes in the news

Baby bottle dish soap recalled due to harmful bacteria in the soap – ABC Action News

Microbes on the market

This Biotech Clothing Automatically Ventilates When You Start to Sweat – Kyree Leary – Futurism

August 24, 2017

Bacterial paleontology of iron formations, gene expression from bacteria and archaea in the Amazon River, indoles promote a “youthful” gene expression profile in their host.

Events and jobs

Podcast: Branding Bacteria – Carla Brown

General microbiome

Preprint: Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding through Extensive Gene Loss – Colin P McNally – bioRxiv

Pregnancy and early life

Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition – Alexandra R Sitarik – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Increased Tryptophan Metabolism is Associated With Activity of Inflammatory Bowel Diseases – Susanna Nikolaus – Gastroenterology

Animal experiments

Indoles from commensal bacteria extend healthspan – Robert Sonowal – PNAS

Plant, root, and soil microbiome

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities – Alessandro Florio – Scientific Reports

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China – Yun Xiang – International Journal of Environmental Research and Public Health

Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island – Giuseppe Concheri – Scientific Reports

Influence of film mulching on soil microbial community in a rainfed region of northeastern China – Wenyi Dong – Scientific Reports

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE) – Serena Fraraccio – Scientific Reports

Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences – Ran Zhao – The ISME Journal

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey – Lu Zhang – FEMS Microbiology Ecology

Water and extremophile microbiome

Predicting blooms of toxic cyanobacteria in eutrophic lakes with diverse cyanobacterial communities – Aleksandra Bukowski – Scientific Reports

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River – Brandon M Satinsky – Frontiers in Marine Science

Probiotics/prebiotics

Protocol for a randomised, placebo-controlled pilot study for assessing feasibility and efficacy of faecal microbiota transplantation in a paediatric ulcerative colitis population: PediFETCh trial – Nikhil Pai – Gastroenterology and Hepatology

More microbes

Bacterial paleontology of the Neoarchean banded iron formations of Karelia and the Kola Peninsula – M M Astafieva – Paleontological Journal

Microbes in the news

Cyborg bacteria covered in solar panels can beat plants at photosynthesis – Angela Chen – The Verge

Gut bacteria influence the brain indirectly, study shows – Maria Cohut – Medical News Today

Scientists uncover two-layer identification among soil bacteria – Amy Wallace – UPI.com

We May Have Just Found The Hormone That Lets Gut Bacteria Talk to The Brain – Peter Duckbill – Science Alert

August 3, 2017

The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

July 20, 2017

A study of chemical interactions between fungi and ants by imaging mass spectrometry, characterization of forty-six Arthrobacter phages, influence of fruit fungal infestation on vertebrate fruit preferences.

Human gut microbiome

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003 – Lorena Ruiz – Scientific Reports

Animal experiments

Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity – Francesco Suriano – Scientific Reports

Effects of dietary supplementation with two alternatives to antibiotics on intestinal microbiota of preweaned calves challenged with Escherichia coli K99 – Yanliang Bi – Scientific Reports

Animal microbiome

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants – Cristopher A Boya P – Scientific Reports

Plant, root, and soil microbiome

Population structure of an orchid mycorrhizal fungus with genus-wide specificity – M P Ruibal – Scientific Reports

Water and extremophile microbiome

Review: Cultivation of microbes from the deep-sea environments – Zenghu Zhang – Deep Sea Research Part II: Topical Studies in Oceanography

Food microbiology

Fungal infestation boosts fruit aroma and fruit removal by mammals and birds – Josep E Peris – Scientific Reports

Pre-print: Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – bioRxiv

Probiotics/prebiotics

Dietary lipid content reorganizes gut microbiota and probiotic L. rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish – Silvia Falcinelli – Scientific Reports

Phages and viruses

Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages – Karen K Klyczek – PLOS ONE

Pre-print: Isolation and characterization of BpL1, a broad acting lytic bacteriophage against Brucella – Vimlesh Gupta – bioRxiv

Microbes in the news

Bac-for good: Bacteria passed between generations benefits you more than others – Phys.org

Microbes on the market

Verily Releases Bacteria-Infected Mosquitoes To Fight Zika And Dengue: Is Wolbachia Technique Safe For Humans? – Allan Adamson – Tech Times

Science, career, and publishing

Climate scientists flock to France’s call – Declan Butler – Nature

July 6, 2017

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

June 22, 2017

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