September 22, 2016

Secretor status of mother affects infant’s gut microbiota development, differences between lean and obese kids, effect of ozone levels on plant microbiomes.

Pregnancy and early life

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study – Paula Smith-Brown – PLOS ONE

Press: Research reveals importance of breast milk gene for toddler gut bacteria – University of Queensland

Human vaginal microbiome

Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota – Christina Gill – PLOS ONE

Human urinary tract microbiome

Review: Urinary incontinence: Making sense of the urinary microbiota in clinical urology – Gregor Reid – Nature Reviews Urology

Human gut microbiome

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio

Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth – Martina Goffredo – Journal of Clinical Endocrinology & Metabolism

Press: Gut bacteria differ between obese and lean youth – MedicalXpress
Fat Flora? Gut Bacteria Differ in Obese Kids – Christopher Wanjek – LiveScience

Conference poster: Unique Gut Microbiome Triggers Ankylosing Spondylitis, Research Hints – Nancy A. Melville – Medscape

Review: The Microbiome: a Revolution in Treatment for Rheumatic Diseases? – James T. Rosenbaum – Current Rheumatology Reports

Review: Gut Instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration – Timothy G. Dinan – The Journal of Physiology

Animal models

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis – Marlies Meisel – The ISME Journal

Animal microbiome

In situ visualization of bacterial populations in coral tissues: pitfalls and solutions – Naohisa Wada – PeerJ

Plant, root, and soil microbiome

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice – Yoshiaki Ueda – PLOS ONE

Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang – Rajal Debnath – Frontiers in Plant Science

Does cryptic microbiota mitigate pine resistance to an invasive beetle-fungus complex? Implications for invasion potential – Chihang Cheng – Scientific Reports

Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics – C. Sheridan – Microbial Ecology

Review: The Plant Microbiota: Systems-Level Insights and Perspectives – Daniel B. Müller – Annual Review of Genetics

Water microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta – Wei Cai – Wter Science & Technology

Metagenomics and bioinformatics

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

TreeScaper: visualizing and extracting phylogenetic signal from sets of trees – Wen Huang – Molecular Biology and Evolution

Techniques

Microbial community analysis using MiSeq sequencing in a novel configuration fluidized bed reactor for effective denitrification – Phatchariya Rungkitwatananukul – Bioresource Technology

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq – Catherine M. Burke – PeerJ

More microbiology

A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time – Josef C. Uyeda – PLOS ONE

Microbes in the news

The Perks of Manipulating the Microbiome: Probiotics, poop pills and … – Lynne Peeples – Gastroenterology & Endoscopy News

About paper that came out in June: The Breast Has Its Own Microbiome—and the Mix of Bacteria could Prevent or Encourage Cancer – Knvul Sheikh – Scientific American

Plants take it all in to deal with bacteria – Science Daily

Purdue scientists have bright idea for detecting harmful bacteria in food products – Purdue University

UCR professor discovers bacterial connection between wild bees and flowers – Som Chaturvedi – The Highlander (belongs to this paper)

Microbes and money

Skin Microbiome Company Mother Dirt Launches First-Ever Biome-Friendly Moisturizer
AOBiome’s consumer division expands skin product line to complement signature AO+Mist – PR Newswire

Science, publishing, and career

Sad outcome of survey: “Although the majority of department chairs value educational scholarship, only a minority perceive value in faculty blogging effort”. Does Academic Blogging Enhance Promotion and Tenure? A Survey of US and Canadian Medicine and Pediatric Department Chairs – Christian Blake Cameron

September 19, 2016

Posted on September 19, 2016 by eliesbik

Effects of siblings on infants’ microbiotas, kids with end-stage renal disease, gut microbiota of 4 termite species.

Pregnancy and early life

Association of household siblings with nasal and fecal microbiota in infants – Kohei Hasegawa – Pediatrics International

Human respiratory microbiome

Review: Linking Microbiota and Respiratory Disease – Matthias Hauptmann – FEBS Letters

Human blood ‘microbiome’

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis – Benjamin Lelouvier – Hepatology

Human gut microbiome

Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study – Janice Crespo-Salgado – Microbiome

Review: Interaction between gut microbiota and toll-like receptor: from immunity to metabolism – Jensen H.C. Yiu – Journal of Molecular Medicine

Animal and in vitro experiments

An intestinal microbiota-farnesoid X receptor axis modulates metabolic disease – Frank J. Gonzalez – Gastroenterology

Review: Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids – Sina Bartfeld – Developmental Biology

Animal microbiome

Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites – LiJuan Su – Journal of Insect Science

Plant, root, and soil microbiome

Rare taxa maintain microbial diversity and contribute to terrestrial community dynamics throughout bark beetle infestation – Kristin M. Mikkelson – Applied and Environmental Microbiology

More microbes

Microbial herd protection mediated by antagonistic interaction in polymicrobial communities – Megan Wong – Applied and Environmental Microbiology

Microbes in the news

Attack of the plastic eaters: Can mushrooms, bacteria and mealworms save the planet from pollution? – Diane Stopyra – Salon

Harnessing the amazing work of the 40 trillion chemists in your gut microbiome – Emily P. Balskus – STAT News

Microbiome Companies Attract Big Investments – Brian Gormley – The Wall Street Journal

Mud Pies: Superfood for the Microbiome? – John L. Marshall – MedScape

September 18, 2016

Posted on September 18, 2016 by eliesbik

Gut fermentation bubbles might promote decompression sickness in divers, corals of the Tropical Eastern Pacific, and a new microbiome book: Let Them Eat Dirt.

General microbiome

Review: Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease – Victoria J. Martin – The Journal of Pediatrics

Pregnancy and early life

Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool-age asthma – Leah Stiemsma – Clinical Science

Human oral microbiome

Review: The role of bacteriophages in periodontal health and disease – Graça Pinto – Future Medicine

Human urinary tract microbiome

A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms – Asha Rani – Scientific Reports

Human vaginal microbiome

Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study – Spyros A. Kalams – The European Journal of Contraception & Reproductive Health Care

Human gut microbiome

Gut fermentation seems to promote decompression sickness in humans – Sébastien de Maistre – Journal of Applied Physiology

Review: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease – Francesca Pistollato – Nutrition Reviews

Review: Enteric immunity, the gut microbiome, and sepsis: Rethinking the germ theory of disease – Javier Cabrera-Perez – Experimental Biology and Medicine

Review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Structural modulation of the gut microbiota and the relationship with body weight: compared evaluation of liraglutide and saxagliptin treatment – Lin Wang – Scientific Reports

Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice – Ningwen Tai – Journal of Experimental Medicine

Press: Yale study shows that gut microbes could trigger type 1 diabetes – Jack Woodfield – Diabetes.co.uk

Intestinal immune maturation is accompanied by temporal changes in the composition of the microbiota – G. Den Hartog – Beneficial Microbes

Animal microbiome

First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific – Joicye Hernández-Zulueta – FEMS Microbiology Ecology

Bioinformatics

Reference point insensitive molecular data analysis – M. Altenbuchinger – Bioinformatics

Microbes in the news
New book: Let Them Eat Dirt – B. Brett Finlay and Marie-Claire Arrieta

September 17, 2016

Posted on September 17, 2016 by eliesbik

Metabolic interactions between a 4-species community, captive and wild red-crowned cranes, microbial life around a coal mine fire that’s been burning for over 50 years.

Pregnancy and early life

Associations between EBV and CMV Seropositivity, Early Exposures, and Gut Microbiota in a Prospective Birth Cohort: A 10-Year Follow-up – Claudia Carvalho-Queiroz – Frontiers in Pediatrics

Human oral microbiome

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health – Andres Gomez – Microbial Ecology

Human gut microbiome

Gut microbiota, metabolome and immune signatures in patients with uncomplicated diverticular disease – Giovanni Barbara – Gut

Faecal Concentrations of Short-chain Fatty Acids and Selected Bacteria in Healthy and Celiac Children – Maša Primec – International Journal of Celiac Disease

Animal and in vitro experiments

Impact of Gluten-Friendly Bread on the Metabolism and Function of In Vitro Gut Microbiota in Healthy Human and Coeliac Subjects – Antonio Bevilacqua – PLOS ONE

Protocol: Intestinal Organoids as a Novel Tool to Study Microbes–Epithelium Interactions – Giulia Nigro – Methods in Molecular Biology

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community – Xiaokan Guo – PLOS Computational Biology

Animal microbiome

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis) – Yuwei Xie – Scientific Reports

Compartmentalization of microbial communities that inhabit the hindguts of millipedes – James B. Nardi – Arthropod Structure & Development

Plant, root, and soil microbiome

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils – Luís França – Extremophiles

Niche filtering of bacteria in soil and rock habitats of the Colorado Plateau Desert, Utah, USA – Kevin Lee – Frontiers in Microbiology

The Centralia, PA, coal mine fire has been burning since 1962. Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – PeerJ Preprint

Water and extremophile microbiome

Functional ecology of soil microbial communities along a glacier forefield in Tierra de Fuego (Chile) – Miguel Angel Fernández-Martínez – Frontiers in Microbiology

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia – John Paul Balmonte – Frontiers in Microbiology

Shifts in Microbial Community Structure and Activity in the Ultra-Oligotrophic Eastern Mediterranean Sea Driven by the Deposition of Saharan Dust and European Aerosols – Cui Guo- Frontiers in Marine Science

Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225) – Antje Lauer – Microorganisms

Built environment microbiome

Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants – Damien Costa – Pathogens and Disease

Techniques

Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction – Butler, Ross N. – Journal of Pediatric Gastroenterology and Nutrition

Microbes in the news

Get Your Children Good and Dirty – B. Brett Finlay and Marie-Claire Arrieta – Wall Street Journal

NASA Space Biology Fellowships to Study the Microbiome of the ISS as a Built Environment Research Announcement – SpaceRef

Intercontinental Plant Microbiome Research Earns UBiome Grant – Haverford.edu

Scientific research shows how corrugated stops bacteria – Packaging World

Bacterial Predators Surprise Scientists with Hidden Diversity – Jennifer Frazer – Scientific American

Bacteria Hysteria

Fear-mongering story sponsored by industry, performed by microbiology professor: Petri dishes you can wear: UA researchers study the bacteria on the bottoms of your shoes – Courtney Gallant – The Daily Wildcat

September 15, 2016

Posted on September 15, 2016 by eliesbik

A review on the human skin microbiome, review on therapeutic manipulation of microbiotas, and microbial enzymes around earthworm casts.

Jobs and events

Faculty Positions in Microbiology and Immunology – University of South Alabama College of Medicine

Human respiratory microbiome

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum on Allergy & Rhinology

Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation – Kirsty M. Sands – Journal of Critical Care

Human skin microbiome

Review, will be open access soon: Experimental metagenomics and ribosomal profiling of the human skin microbiome – Pamela Ferretti – Experimental Dermatology

Human gut microbiome

Gut microbiome alterations in patients with stage 4 hepatitis C – AbdelRahman Mahmoud Aly – Gut Pathogens

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Review: Therapeutic Manipulation of the Microbiota: Past, Present and Considerations for the Future – Vincent B. Young – Clinical Microbiology and Infection

Animal experiments

Effects of different diets on intestinal microbiota and nonalcoholic fatty liver disease development – Jian-Ping Liu – World Journal of Gastroenterology

Sex-specific effects of docosahexaenoic acid (DHA) on the microbiome and behavior of socially-isolated mice – Daniel J. Davis – Brain, Behavior, and Immunity

Animal microbiome

Structural differences in gut bacteria communities in developmental stages of natural populations of Lutzomyia evansi from Colombia’s Caribbean coast – Rafael José Vivero – Parasites & Vectors

Plant, root, and soil microbiome

Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts – Jerzy Lipiec – Frontiers in Microbiology

Air microbiome

Influence of Rain on the Abundance and Size Distribution of Bioaerosols –
Chathurika M. Rathnayake – Atmospheric Chemistry and Physics Discussions

Techniques

Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias – Michelle M. O’Donnell – Journal of Microbiological Methods

Application of Next Generation Sequencing Technologies in Revealing Plant-Microbe Interactions – Ramesh Kothari – Journal of Next Generation: Sequencing & Applications

Technical note: Discard the specimen collection swab directly at point of care to improve extensive automated processing in clinical microbiology laboratories – Manuela Avolio – Journal of Microbiological Methods

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janabi – Journal of Microbiological Methods

Microbes in the news

Secrets of life in the soil.Diana Wall has built a career on overturning assumptions about underground ecosystems. Now she is seeking to protect this endangered world – Rachel Cernansky – Nature

Ice machine, sinks linked to Legionnaires’ cases at UW Medical Center – JoNel Aleccia – Seattle Times

Israeli product that pinpoints viruses, bacteria gets European grant – ImmunoXpert is based on the fact that viruses and bacteria stimulate different protein pathways when they infect the body – Judy Siegel-Itzkovich – Jpost.com

A spoonful of sugar helps the bacteria go down. Gel-like layers protect microbes and help them stick to your intestines – Sara Chodosh – Popsci

Bik’s non-microbiology Picks

VA Palo Alto’s spending on artwork blasted – Jacqueline Lee – The Mercury News

September 14, 2016

Posted on September 14, 2016 by eliesbik

Testing antibacterial and antismelly capacities of deodorant with a sniffer panel, uncovering trophic interactions by metagenomic sequencing of ladybugs’ gut contents.

Events

6th ASM Beneficial Microbes meeting, Days 3-4 – Tera Levin – Storify

Human armpit microbiome

Smelly armpits, bacteria, and a sniffer panel: Effective axillary malodour reduction by polyquaternium-16-containing deodorants – B. Traupe – International Journal of Cosmetic Science

Human gut microbiome

Review: Pathogenesis of acute graft-versus-host disease: from intestinal microbiota alterations to donor T cell activation – Robert Zeiser – British Journal of Haemotology

Review: Role of the gut microbiota in host appetite control: bacterial growth to animal feeding behaviour – Sergueï O. Fetissov – Nature Reviews Endocrinology

Animal microbiome

Ladybugs: Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents – Débora P. Paula – PLOS ONE

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

Built Environment microbiome

Previously in preprint, now published: Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ

Techniques / Bioreactors

Quantitative high-throughput population dynamics in continuous-culture by automated microscopy – Jason Merritt – Scientific Reports

Microbes in the news

Genevieve Sullivan: Bacteria and Food Packaging – Darren Chow – Cornell Sun

Samantha VanWees: Bacteria, Light and Milk Processing – Isabelle Philippe – CornellSun

This should be Open Access, because it is just a list of links. But it is not unfortunately: Web Alert: Ecophysiology of anaerobes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett

An arms race with a superbug: Study shows how pneumonia-causing bacteria invade the body – Phys.org

Coming together for microbiology: new network for scientists working in forensic medicine – Labnews UK

The possible link between bacteria and chronic disease? – Jason Tetro – PopSci

See paper in Advanced Materials featured yesterday: Delivering beneficial bacteria to the GI tract. Method that transports microbes through the stomach to the intestine may benefit human health – Anne Trafton – MIT News Office

Science, publishing, and career

Mansplaining: how not to talk to female Nasa astronauts – Laura Bates – The Guardian

September 13, 2016

Posted on September 13, 2016 by eliesbik

Infant gut microbiome and allergy risk, gut microbiome in mice and susceptibility to Plasmodium, microbiome of a stranded striped dolphin, cadavers in Canada, rRNA operon copy numbers.

Events

(repeat posting) 4th Microbiome R&D Business collaboration Forum & Probiotics Congress, October 3-4, 2016, La Jolla,San Diego, USA. Use discount code: ALLONG for a special rate of $399.

Pregnancy and birth

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation – Kei E Fujimura – Nature Medicine

Press: Infant gut microbiome appears to shape allergy risk by altering immune responses – EurekAlert
Newborn gut microbiome predicts later allergy and asthma, study finds. Microbial byproducts link particular early-life gut microbes to immune dysfunction – Science Daily
Clues in microbiome of infants point to future allergies and asthma – Yvette Brazier – Medical News Today
Neonatal Gut Bacteria Might Promote Asthma. Byproducts of gut microbes in some 1-month–old babies trigger inflammation that is linked to later asthma development, researchers find. – Anna Azvolinsky – The Scientist

Human urinary tract microbiome

Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance – Asha Rani – Translational Research

Human gut microbiome

Gut bacterial microbiota in psoriasis: A case control study – Doaa Masallat – African Journal of Microbiology Research

Review: Cognitive Function and the Microbiome – M.G. Gareau – International Review of Neurobiology

Review: Advances in Gut Microbiome Research and Relevance to Pediatric Diseases – Lindsey Albenberg – The Journal of Pediatrics

Animal experiments

Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects – Stefano Levi Mortera – Frontiers in Microbiology

Functional characteristics of the gut microbiome in C57BL/6 mice differentially susceptible to Plasmodium yoelii – Joshua M. Stough – Frontiers in Microbiology

Modulation of the bifidobacterial communities of the dog microbiota by zeolite – Alberto Sabbioni – Frontiers in Microbiology

Animal microbiome

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal – Filipa Godoy-Vitorino – Research in Microbiology

Book Chapter: Microbial Interactions on Coral Surfaces and Within the Coral Holobiont – Max Teplitski – The Cnidaria, Past, Present and Future

Book Chapter: Association of Coral-Microbes, and the Ecological Roles of Microbial Symbionts in Corals – Wei Sun – The Cnidaria, Past, Present and Future

Human Lice in Paleoentomology and Paleomicrobiology – Rezak Drali – ASM Microbiology Spectrum

Plant, root, and soil microbiome

Resource partitioning between bacteria, fungi and protists in the detritusphere of an agricultural soil – Susanne Kramer – Frontiers in Microbiology

Composition and activity of soil microbial communities in different types of temperate forests – Marcin Chodak – Biology and Fertility of Soils

The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth – Małgorzata Baćmaga – Ecotoxicology

Review: Plant microbe interactions in post genomic era: perspectives and applications – Jahangir Imam – Frontiers in Microbiology

Water microbiome

Quantification of viral and prokaryotic production rates in benthic ecosystems: a methods comparison – Eugenio Rastelli – Frontiers in Microbiology

Microbiome of death

Cadavers in Canada: Book Chapter: Changes in Soil Microbial Activity Following Cadaver Decomposition During Spring and Summer Months in Southern Ontario – Heloise A. Breton – Soil in Criminal and Environmental Forensics

Wastewater and pollution microbiology

Poster: MiDAS: A curated database for the microorganisms of activated sludge and anaerobic digesters – Simon Jon McIlroy – Water Engineering and Biofilm IWA Specialist Conference, 2016

Probiotics

Layer-by-Layer Encapsulation of Probiotics for Delivery to the Microbiome – Aaron C. Anselmo – Advanced Materials

Food microbiology

Book: Functional Nucleic Acids Detection in Food Safety: Theories and Applications – Wentao Xu – Springer

Microbial ecology

Aligning the Measurement of Microbial Diversity with Macroecological Theory – James C. Stegen – Frontiers in Microbiology

Editorial: Insights into microbe-microbe interactions in human microbial ecosystems: strategies to be competitive – Nuria Salazar – Frontiers in Microbiology

Bioinformatics and metagenomics

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies – Benjamin R.K. Roller – Nature Microbiology

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers – Michelle Davison – PLOS ONE

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes – Carmen H.S. Chan – Computational Biology and Chemistry

Review: Advances in biodiversity: metagenomics and the unveiling of biological dark matter – Robert J. Robbins – Standards in Genomic Sciences

Microbes in the news

What we have in common with corals and their unexplored microbial world – Alejandra Hernandez – The Conversation

September 12, 2016

Posted on September 12, 2016 by eliesbik

Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 9, 2016

Posted on September 9, 2016 by eliesbik

Microbiome and tuberculosis, mangoes, lessons from amphibians, and the microbiome of buildings.

Human gut microbiome

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection – Ilan Youngster – BMC Medicine

Review: Microbiome Changes during Tuberculosis and Antituberculous Therapy – Bo-Young Hong – Clinical Microbiology Reviews

No consensus on how the microbiome affects tuberculosis, review finds – Science Daily

Animal models

Screen Shot 2016-09-09 at 8.19.34 AM.png

Mango, “hedgehog” style – Wikipedia

Mango Supplementation Modulates Gut Microbial Dysbiosis and Short-Chain Fatty Acid Production Independent of Body Weight Reduction in C57BL/6 Mice Fed a High-Fat Diet – Babajide Ojo – Journal of Nutrition

Mango and the Microbiota: New Research Reveals Potential Role of this Superfruit in Maintaining Gut Health – National Mango Board – PR Newswire

Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats – Hirokazu Sato – Gastroenterology

Press (with ugly title): The influence of fat when gut bacteria is reduced by antibioticsm – Science Daily

Animal microbiome

Harnessing the Microbiome to Prevent Fungal Infections: Lessons from Amphibians – Jenifer B. Walke – PLOS Pathogens

Built environment microbiome

Ten questions concerning the microbiomes of buildings – Rachel I. Adams – Building and Environment

The hot new 10 questions concerning the microbiomes of buildings will surprise you – Jonathan Eisen – MicroBEnet

Microbes in the news

“I’ll never let go, Jack I promise”
Titanic expected to disappear by 2030 thanks to hungry bacteria – Matthew Humphries – Geek.com
Video: Will Bacteria Completely Destroy The Titanic’s Remains? – MSN Video

Scientists find deadly scrub typhus bacteria in South America – Reuters

Mount Sinai Beth Israel Says Legionella Bacteria Found in Several Areas of Hospital – NY1.com

Mood, mind and memory: can gut bacteria meddle with the brain? – Dyani Lewis – Cosmos Magazine
Bugs as drugs – medicine’s next frontier – Dyani Lewis – Cosmos Magazine

Driving Microbiome Science: PKU and Probiotics – Raredr

Experts urge a defensive stance in efforts against antimicrobial resistance – EurekAlert

Microbes and money

Microban Opens Microbiology Testing Services to Non-Partners – Genevieve Scarano – Sourcing Journal

Science, publishing, and career

Your toughest experiment: taking the lead in the lab. Eight scientists share the secrets of being a successful PI – Times Higher Education

	Francis W on The Hetch Hetchy Railroad
	Best Practice Exchan… on June 1, 2018
	May 17, 2024 \| Micro… on May 15, 2024
	Kathy Brown on The Hetch Hetchy Railroad
	John Wilbur on The Hetch Hetchy Railroad

Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Animal microbiome

September 22, 2016

September 21, 2016

September 19, 2016

September 18, 2016

September 17, 2016

September 15, 2016

September 14, 2016

September 13, 2016

September 12, 2016

September 9, 2016