Category Archives: Pregnancy and birth

September 28, 2016

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Twins, body fat, and bacteria, dietary zinc and C. diff infections, honey inhibits biofilm formation, microbial life in a Great Lake sinkhole.

Pregnancy and early life

Review: The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life -William B. Miller Jr. – Frontiers in Pediatrics

Human gut microbiome

Heritable components of the human fecal microbiome are associated with visceral fat – Michelle Beaumont – Genome Biology

Press: Body fat link to bacteria in faeces – BBC
How Gut Bacteria May Predict Belly Fat – Alice Park – Time

Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis – Kentaro Iwasawa – Gut

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

Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection – Joseph P Zackular – Nature Medicine

Editorial: Devil in the detail: A closer look at childhood obesity and the gut microbiota – Michael W. Taylor – Environmental Microbiology

News and views: Culturing: Looking it up in our gut – Clarisse Marotz – Nature Microbiology

Animal microbiome

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice – Taichi A. Suzuki – PLOS ONE

Plant, root, and soil microbiome

Using a Control to Better Understand Phyllosphere Microbiota – Andrea R. Ottesen – PLOS ONE

Caves: Microbial contributions to subterranean methane sinks – J. T. Lennon – Geobiology

Diatom blooms and associated vegetation shifts in a subarctic peatland: responses to distant volcanic eruptions? – U. Kokfelt – Journal of Quaternary Science

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant – Gianna Pitsch – The Journal of Eukaryotic Microbiology

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi – Xihui Xu – PLOS ONE

Fungal Endophytes as a Metabolic Fine-Tuning Regulator for Wine Grape – Ming-Zhi Yang – PLOS ONE

Water and extremophile microbiome

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole – L. E. Kinsman-Costello – Geobiology

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes – Jan-Hendrik Hehemann – Nature Communications

Proteomics

The impact of sequence database choice on metaproteomic results in gut microbiota studies – Alessandro Tanca – Microbiome

More microbiology

Diluted honey inhibits biofilm formation: potential application in urinary catheter management? – Somadina Emineke – Journal of Clinical Pathology

Press: Manuka honey may help prevent life-threatening urinary infections – Simon Hendel – The Conversation
Honey May Be a Natural Way to Beat Bacteria – Alexandra Sifferlin – Time

Personalized therapeutic cocktail of wild environmental phages rescues mice from A. baumannii wound infections – James M. Regeimbal – Antimicrobial Agents and Chemotherapy

Press: A Cocktail Of Wild Viruses Treats Bacterial Wound Infections In Mice – Alex Berezow – American Council on Science and Health

Microbes in the news

Chicago Shedd Aquarium Studies Microbes’ Effect on Sea Life – Illumina

The 3 Robs: NIH Funds Research to See if Gut Microbiomes of Hispanics/Latinos Influence Their Diabetes Risk – Albert Einstein College of Medicine

Antibiotic resistance can occur naturally in soil bacteria – Science Daily

Science, publishing, and career / Peer review

Author affiliation can bias peer review: Single-blind vs Double-blind Peer Review in the Setting of Author Prestige – Kanu Okike – JAMA

September 27, 2016

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Pediatric multiple sclerosis,  Hydra as a microbiome model, species from bat feces, textile wastewater, and sample preparation for metabolomics.

Events

HIV Microbiome Workshop 2016, November 17-18, 2016, NIH Campus, Bethesda, MD. Here is the program

Pregnancy and early life

Association of Chorioamnionitis with Aberrant Neonatal Gut Colonization and Adverse Clinical Outcomes – Kriti Puri – PLOS ONE

Human respiratory microbiome

Translational Aspects of the Human Respiratory Virome – Alicia B Mitchell – American Journal of Respiratory and Critical Care Medicine

Human skin and gut microbiome

The role of skin and gut microbiota in the development of atopic eczema – T. Marrs – British Journal of Dermatology

Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls – Helen Tremlett – BMC Neurology

Intestinal Dysbiosis and Yeast Isolation in Stool of Subjects with Autism Spectrum Disorders – Maria Rosaria Iovene – Mycopathologia

Interactions between Obesity Status and Dietary Intake of Monounsaturated and Polyunsaturated Oils on Human Gut Microbiome Profiles in the Canola Oil Multicenter Intervention Trial (COMIT) – Shuaihua Pu – Frontiers in Microbiology

Review: Diet Influence on the Gut Microbiota and Dysbiosis related to Nutritional Disorders – Maryam Tidjani Alou – Human Microbiome Journal

Review: Role of the Intestinal Microbiota in Host Responses to Stressor Exposure – A.R. Mackos – International Review of Neurobiology

Review: Exploring relationships between host genome and microbiome: new insights from genome-wide association studies – Muslihudeen A. Abdul-Aziz – Frontiers in Microbiology

Animal models

Vitamin D and allergic airway disease shape the murine lung microbiome in a sex-specific manner – Michael Roggenbuck – Respiratory Research

Perspective: Transitioning from microbiome composition to microbial community interactions: the potential of the metaorganism Hydra as an experimental model – Peter Deines – Frontiers in Microbiology

Animal microbiome

Bats: Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples – Faith M. Walker – PLOS ONE

Symbionts modify interactions between insects and natural enemies in the field – Jan Hrček – Journal of Animal Ecology

Plant, root, and soil microbiome

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait – Kevin Panke-Buisse – Microbial Ecology

Effects of Artificial Soil Aeration Volume and Frequency on Soil Enzyme Activity and Microbial Abundance when Cultivating Greenhouse Tomato – Yuan Li – Soil Science Society of America Journal

Water and pollution microbiome

Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community – Jaejin Lee – Marine Pollution Bulletin

Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants – Ken Meerbergen – MicrobiologyOpen

Metabolomics

Sample preparation procedures utilized in microbial metabolomics: an overview – Małgorzata Patejko – Journal of Chromatography B

More microbiology

The quest for the minimal bacterial genome – Esteban Martínez-García – Current Opinion in Biotechnology

Microbes in the news

Inaugural lecture will explore some microbes’ invisible war on humans – University of Kansas

 

September 21, 2016

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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

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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

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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 13, 2016

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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

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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 2, 2016

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Correlation between oligosaccharides and gut microbes in infants, metabolic pathways in 10 infant twin pairs, an Open-Source alternative for USEARCH, and an important new FDA rule.

Events

Unfortunately, all of the confirmed speakers are men. Nature Conference on Environmental and Human Microbiomes: Drivers of Future Sustainability, February 12-15, 2017, Singapore

Pregnancy and birth

Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community – Jasmine C. C. Davis – Molecular & Cellular Proteomics

Membrane Vesicles of Group B Streptococcus Disrupt Feto-Maternal Barrier Leading to Preterm Birth – Manalee Vishnu Surve – PLOS Pathogens

Press: Bacteria linked to stillbirth: mouse study – Sarah Wiedersehn – Australian Associated Press

Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins – Shaoming Zhou – PLOS ONE

A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders – Ryo Inoue – Bioscience, Biotechnology, and Biochemistry

Human gut microbiome

Commentary: Gut microbiota: Changes in gut microbes and host metabolism: squaring the circle? – Patrice D. Cani – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Bacterial diversity of the American sand fly Lutzomyia intermedia using high-throughput metagenomic sequencing – Carolina Cunha Monteiro – Parasites & Vectors

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea – Mamoon M.D. Al-Rshaidat – Genome

Plant, root, and soil microbiome

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes – Agnieszka Wolińska – Microbial Ecology

Water microbiome

Microbial diversity within the Trichodesmium holobiont – Mónica Rouco – Environmental Microbiology

Bioinformatics and metagenomics

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures – Samuele Girotto – Bioinformatics

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units – Matthew A. Jackson – PeerJ

An Open Source alternative for USEARCH: VSEARCH: a versatile open source tool for metagenomics – Torbjørn Rognes- PeerJ Preprint

Using viromes to predict novel immune proteins in non-model organisms – Steven D. Quistad – Proceedings of the Royal Society B

Microbes in the news

FDA issues final rule on safety and effectiveness of antibacterial soaps. Rule removes triclosan and triclocarban from over-the-counter antibacterial hand and body washes – FDA

FDA bans antibacterial soaps; “No scientific evidence” they’re safe, effective
Ban includes soaps with any of 19 chemicals, including triclosan – Beth Mole – ArsTechnica

Living Russian Dolls.They have bacteria in their cells, and smaller bacteria in those bacteria—and that’s not even the weirdest bit – Ed Yong – The Atlantic

Sydney scientists accidentally discover antibiotic to treat koalas with chlamydia – Matt Wordsworth – ABC Australia

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

August 29, 2016

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Breast milk protects against GBS colonization, niche segregation in the gut, drug detection and effects in streams, reconstruction of metabolic networks.

Pregnancy and birth

Role of human milk oligosaccharides in Group B Streptococcus colonisation – Nicholas J Andreas – Clinical & Translational Immunology

Press: Breast Milk Sugar May Protect Newborns Against Deadly Bacterial Infection – Dianne Depra – Tech Times

Human skin microbiome

News and Views: Microbiome: Ecology of eczema – Ian D. Odell – Nature Microbiology

Human respiratory microbiome

Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis – Urszula Kosikowska – BMC Infectious Diseases

Human vaginal microbiome

The cervico-vaginal microbiota in women notified for Chlamydia trachomatis infection: A case-control study at the STI outpatient clinic in Amsterdam, the Netherlands – C van der Veer – Clinical Infectious Diseases

Human gut microbiome

Transcriptional interactions suggest niche segregation among microorganisms in the human gut – Damian Rafal Plichta – Nature Microbiology

Review: Alzheimer’s disease and gut microbiota – Xu Hu – Science China Life Sciences

Review: In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut – A.J. Hay – Advances in Applied Microbiology

Animal experiments

Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model – Aaron M.T. Barnes – Virulence

Animal microbiome

Distinct Bacterial Microbiomes in Sexual and Asexual Potamopyrgus antipodarum, a New Zealand Freshwater Snail – Cristina Takacs-Vesbach – PLOS ONE

Water and extremophile microbiome

Occurrence and Potential Biological Effects of Amphetamine on Stream Communities – Sylvia S. Lee – Environmental Science & Technology

Press: Ecological consequences of amphetamine pollution in urban streams – Cary Institute
Your drain on drugs: Amphetamines seep into Baltimore’s streams – Jen Christensen – CNN
Comment from PubMed Commons by Daniel Himmelstein 

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4950 m, in Venezuelan tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Metabolomics

Efficient Reconstruction of Predictive Consensus Metabolic Network Models – Ruben G. A. van Heck – PLOS Computational Biology

Bioinformatics and Metagenomics

Review: Toward Accurate and Quantitative Comparative Metagenomics – Stephen Nayfach – Cell

Techniques

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life – Soeren M Karst – bioRxiv

A method for assessing efficiency of bacterial cell disruption and DNA release – Olle M. de Bruin – BMC Microbiology

Microbes in the news

Findings from the American Physiological Society’s Inflammation, Immunity and Cardiovascular Disease conference: Targeting gut bacteria to reduce weight gain – Science Daily

Microbes at work in your Kimchi – Jennifer – The Microbial Menagerie

Artist’s 46-year-old loo paper to be studied: Billy Apple’s decades-old lavatory paper is now part of a scientific study at Auckland University – Jamie Morton – NZ Herald

BacteriaHysteria: The ultimate embodiment of modern day germophobia: Squix – Jonathan Eisen – MicroBEnet

Science misconduct

Leading scientist suspended amid misconduct claims: Robert Ryan, award-winning Scottish microbiologist now under investigation – Victoria Weldon – Herald Scotland

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science