Category Archives: Pregnancy and birth

August 25, 2016

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Microbiome of the Graduate Student Gut, allergic cats, tree phyllosphere, milk tanker trucks, and microbes of soda lakes.

Pregnancy and birth

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

General microbiome

Now published after preprint earlier this year and article in Cell: Revised Estimates for the Number of Human and Bacteria Cells in the Body – Ron Sender – PLOS Biology

Enemies and brothers in arms: Candida albicans and gram-positive bacteria – Toni M. Förster – Cellular Microbiology

Human respiratory microbiome

General antibiotic exposure is associated with increased risk of developing chronic rhinosinusitis – Alice Z. Maxfield – The Laryngoscope

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease – Jeffrey M. Flynn – PLOS Pathogens

Human gut microbiome

Master Thesis: Characterizing Microbiome Changes in the Graduate Student Gut – Justin Roy Lund – University of Oklahoma

Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease – Baohong Wang – Scientific Reports

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System – Long Liu – Scientific Reports

Is there a role for stool metabolomics in cystic fibrosis? – Nadeem O Kaakoush – Pediatrics International

Animal microbiome

Allergic to humans? Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing – Courtney Meason-Smith – Veterinary Dermatology

Fish: The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874) – Xuemei Li – BMC Microbiology

Plant, root, and soil microbiome

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species – Isabelle Laforest-Lapointe – PeerJ

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance – Nick A. Cutler – Microbial Ecology

Autochthonous Microbiota in Arsenic-Bearing Technosols from Zemianske Kostoľany (Slovakia) and Its Potential for Bioleaching and Biovolatilization of Arsenic – Alexandra Šimonovičová – Water, Air, & Soil Pollution

Built environment microbiology

Fungi and Bacteria in Indoor Cultural Heritage Environments: Microbial-related Risks for Artworks and Human Health – Enza Di Carlo – Environment and Ecology Research

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

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of fifteen German biogas plants – Thorsten Schauss – Journal of Applied Microbiology

Food microbiology

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility – Mary E. Kable – mBio

Water and extremophile microbiome

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons – Isabel Ferrera- Frontiers in Marine Science

Book Chapter: Bacteria, Archaea and Viruses of Soda Lakes – William D. Grant – Soda Lakes of East Africa

Bioinformatics and metagenomics

ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

Techniques

Protocols.io: Virtual Communities for Protocol Development and Discussion – Leonid Teytelman – PLOS Biology

More microbiology

The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

How Designers and Scientists Are Using Bees to Map NYC’s Microbes – Liz Stinson – Wired

Graphic novel about World War I depicts gross realities of dysentery – Carolyn Webb – The Age Victoria

The newest food trend: fermentation – Ted Weesner – Boston Globe

 

 

August 12, 2016

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On vacation, so here is a short and late Digest for you: Metabolomics of preterm birth, mouse gut bacteria collection, bacteria associated with mosses.

Pregnancy and birth

Use of metabolomics for the identification and validation of clinical biomarkers for preterm birth: Preterm SAMBA – Jose G. Cecatti – BMC Pregnancy and Childbirth

Animal microbiome

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota – Ilias Lagkouvardos – Nature Microbiology

First public collection of bacteria from the intestine of mice. Mouse gut bacteria find a new home – Science Daily

Environment shapes the fecal microbiome of invasive carp species – Jessica J. Eichmiller – Microbiome

Plant, root, and soil microbiome

Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing – Yang Tian – Journal of Basic Microbiology

Water microbiome

A metabolomics guided exploration of marine natural product chemical space – Dimitrios J. Floros – Metabolomics

Bioreactor microbiome

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates – Irena Maus – Biotechnology for Biofuels

Food microbiology

Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation – Edward D. Kerr – PeerJ

Microbial Ecology and other

Compartmentalization in PVC super-phylum: evolution and impact – Sandrine Pinos – Biology Direct

Conflicts over host manipulation between different parasites and pathogens: Investigating the ecological and medical consequences – Nina Hafer – BioEssays

Microbes in the news

Soil Has a Microbiome, too. The unique mix of microbes in soil has a profound effect on which plants thrive and which ones die – Carrie Arnold – Smithsonian

Gut bacteria have own circadian clock – MedicalXpress

Not your momma’s microbe lab: a new genetic engineering machine takes microbial design to the masses – Casey Gilman – Philly.com

How brushing your teeth could prevent cancer: Twice daily scrub reduces bacteria linked to bowel tumours – Colin Fernandez – Daily Mail

Picture of the day: Metal-oxidizing bacteria from a gold mine – Science 360

Attendee Shares Experience from DDW® 2016 Active Learning Session on the Gut Microbiome – Gasto.org

Science, publishing, and career

The manterruption is real. Why Women Talk Less Than Men at Work – Alicia Adamczyk – Time / Money Magazine

Satire: First Draft of Peer-Review Rebuttal Just Says “Fuck Off” – The Allium

 

 

August 10, 2016

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Maternal high-fat diet and infant gut microbiome.

Pregnancy and birth

The early infant gut microbiome varies in association with a maternal high-fat diet – Derrick M. Chu – Genome Medicine

Press: Maternal high-fat diet during pregnancy can affect baby’s gut microbesMaternal high-fat diet during pregnancy can affect baby’s gut microbes – Dipali Pathak – Baylor College of Medicine

Human gut microbiome

Review: Microbiota and Neurological Disorders: A Gut Feeling – Walter H Moos – BioResearch Open Access

Press: How do the bugs in your gut affect neurodegenerative and psychiatric diseases? – EurekAlert

Animal experiments

Midgut microbiota and host immunocompetence underlie Bacillus thuringiensis killing mechanism – Silvia Caccia – PNAS

Plant, root, and soil microbiome

Yeast Biodiversity in Vineyard Environments Is Increased by Human Intervention –
João Drumonde-Neves – PLOS ONE

Microbes in the news

NIH grants $1.8 million for gut microbiome research in obesity, metabolic syndrome – Healio

How The Microbes Inside Us Went From Enemies To Purported Superhealers – Carolyn Beans – NPR

The poop scientist of Japan – and his dream toilet – Sanjena Sathian – Ozy

Gut Bacteria Mind Their Own Clock, Respond to Melatonin – Clinical Oncology

New model sheds light on secondary bacterial pneumonia – EurekAlert

Science, publishing, and career

Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference? – Anna Kaatz – Academic Medicine

The Government is Shortchanging Our Best Lady Scientists – Madison Pauly – Mother Jones

August 6, 2016

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Airwair microbiome at birth, fungi on strawberries, molds in a library.

Pregnancy and birth

The Airway Microbiome at Birth – Charitharth Vivek Lal – Scientific Reports

Press: Discovery of Infants’ Airway Microbiomes May Help Predict Lung Disease
A newborn’s airway — once thought to be sterile until after birth — is colonized by bacteria– University of Alabama at Birmingham
Discovery of infants’ airway microbiomes may help predict lung disease – Jeff Hansen – Medical Xpress

Gestational Diabetes is associated with changes in Placental Microbiota and Microbiome – Judit Bassols – Pediatric Research

Human respiratory microbiome (also see Pregnancy and Birth)

Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features – Guoqin Yu – Genome Biology

High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors – Daniela Janek – PLOS Pathogens

Human ear microbiome

Molecular microbiological profile of chronic suppurative otitis media – Michel Neeff – Journal of Clinical Microbiology

Human gut microbiome

Antibiotic-Induced Gut Microbiota Disruption Decreases TNF-α Release by Mononuclear Cells in Healthy Adults – Jacqueline M. Lankelma – Clinical and Translational Gastroenterology

Review: Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders – Alper Evrensel – Clinical Psychopharmacology and Neuroscience

Review: Interactions between the gut microbiome and the central nervous system and their role in schizophrenia, bipolar disorder and depression – Adrian Andrzej Chrobak – Archives of Psychiatry and Psychotherapy

Animal microbiome

Strain diversity and host specificity in a specialized gut symbiont of honey bees and bumble bees – J. Elijah Powell – Molecular Ecology

Flow cytometric enumeration of bacterial in the coral surface mucus layer – Yvan Bettarel – Journal of Microbiological Methods

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank – Tanya Brown – PeerJ Preprint

Plant, root, and soil microbiome

Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs – Ahmed Abdelfattah – PLOS ONE

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon-availability in Mediterranean semiarid soils – Felipe Bastida – Molecular Ecology

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem – Allison M. Veach – Molecular Ecology

Review: Phytoremediation: state-of-the-art and a key role for the plant microbiome in future trends and research prospects – Sofie Thijs – International Journal of Phytoremediation

Review: Bacterial pathogenesis of plants: future challenges from a microbial perspective. Challenges in Bacterial Molecular Plant Pathology – Sebastian Pfeilmeier – Molecular Plant Pathology

Review: Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments – Lucie Musilova – Int J Mol Sci

Water and extremophile microbiome

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Meltwater export of prokaryotic cells from the Greenland Ice Sheet – Karen A. Cameron – Environmental Microbiology

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas – Haixia Zhou – Frontiers in MIcrobiology

Review: Extremophilic adaptations and biotechnological applications in diverse environments – James Charlesworth – AIMS Microbiology

Built environment microbiome

Detection of volatile metabolites of moulds isolated from a contaminated library – Anna Micheluz – Journal of Microbiological Methods

Review: Shoe soles as a potential vector for pathogen transmission: A systematic review – Tasnuva Rashid – Journal of Applied Microbiology

Bioinformatics and metagenomics
PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories – Victor Hanson-Smith – PLOS Computational BIology

The Phylogenetic LASSO and the Microbiome – Stephen T Rush – arXiv

Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management – Ravin Poudel – Phytopathology

Techniques

On the study of microbial transcriptomes using second- and third-generation sequencing technologies – Sang Chul Choi – Journal of Microbiology

Microbes in the news

Notre Dame Researcher Explores Bacteria beyond the Ability of Typical Hospital Setting: Gail Weaver – Nina Welding – Engineering

 

August 2, 2016

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Microbial mercury in Antarctic sea ice, bacteria and magnetic field, and what is living in your showerhead.

Events and jobs

Microbiomes of the Built Environment – Meeting #3  (will also be web-casted) – Monday October 17, 2016, at UC Irvine, CA

Postdoctoral position in microbial physiology/environmental microbiology, self-healing concrete, Aarhus University Denmark – Science Careers

General microbiome

Philosophical Transactions of the Royal Society B themed issue: ‘From DNA barcodes to biomes’
A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring – Mehrdad Hajibabaei
Dissecting host-associated communities with DNA barcodes – Christopher C. M. Baker
Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches – Rebecca Yahr
Insect symbionts in food webs – Ailsa H. C. McLean

Pregnancy and birth

Review: The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review – Erigene Rutayisire – BMC Gastroenterology

Human (and animal) oral microbiome

Review: Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals: A Comparative Review – Eric M. Davis – Journal of Veterinary Dentistry

Human respiratory microbiome

Association between Staphylococcus aureus nasal carriage and disease phenotype in patients affected by systemic lupus erythematosus – Fabrizio Conti – Arthritis Research & Therapy

Human gut microbiome

Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population – Zongxin Ling – Scientific Reports

Animal experiments

Chronic Repression of mTOR Complex 2 Induces Changes in the Gut Microbiota of Diet-induced Obese Mice – Mi-Ja Jung – Scientific Reports

Plant, root, and soil microbiome

Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites – Julie Foulon – Science of the Total Environment

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies – James C. Stegen – Scientific Reports

Water and extremophile microbiome

Microbial mercury methylation in Antarctic sea ice – Caitlin M. Gionfriddo – Nature Microbiology

Press: Antarctic sea ice may be a source of mercury in southern ocean fish and birds – Phys.org

Magnetic properties of iron minerals produced by natural iron- and manganese-reducing groundwater bacteria – Alexandra Abrajevitch – Geophysical Journal International

Press: Bacteria Preserve Record of Earth’s Magnetic Fields – EOS

Evidence of small-scale spatial structuring of phytoplankton alpha- and beta-diversity in the open ocean – Erik Askov Mousing – Journal of Ecology

Food microbiology

Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type – Z. Zhong – Journal of Dairy Science

Viruses and phages

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing – Jaime Iranzo – mBio

Bioinformatics and metagenomics/metabolomics

Updated version: GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv

Microbes in the news

Is your gut making you sick?. New research suggests that the range and quantity of microbes that live in our guts could have a powerful effect on a range of conditions including depression, MS and obesity – Ann Robinson – The Guardian

How purple bacteria could help save amphibians in the Rockies : A Colorado researcher is using boreal toads’ microbiomes to help them ward off a deadly fungus – Krista Langlois – High Country News

A short and weird story: Bacteria Filled Water Almost Sends ‘Naked and Afraid’ Contestant Home – Natalie D’Alacio – Yahoo News

Your Showerhead Is Crammed Full of Bacteria That Scientists Want to Study – Kate Lunau – Motherboard

If You Had Really Good Eyesight, Could You See a Single Bacterium? – Julie Taylor – uBiomeBlog

Letter: The microbiologist who didn’t wash his hands after urinating – Peter Dawson – The Guardian

Women more likely to die from bacterial blood infection – Adrian O’Dowd – OnMedica

Sham Poo Washes Out. A bacterial pill that tried to duplicate the benefits of a fecal transplant has failed a clinical trial. What does that mean for the microbiome field? – Ed Yong – The Atlantic

Science, publishing, and career

Not “Pulling up the Ladder”: Women Who Organize Conference Symposia Provide Greater Opportunities for Women to Speak at Conservation Conferences – Stephanie Sardelis – PLOS ONE

In Australia: Stella Count: Women write twice as many books as men, but receive less than half the reviews – Daisy Dumas – Daily Life

 

July 30, 2016

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Honey bee gut microbiome altered by pesticides, colobine primates, sulfur vents, bioaerosol, failed microbiome spore transplant trial.

Events

London Microbiome Workshop – September 7th 2016, Royal College of Physicians, London

Pregnancy and birth

Antibiotic perturbation of the preterm infant gut microbiome and resistome – Andrew J. Gasparrini – Gut Microbes

Multisite microbiome

Acquisition of a high diversity of bacteria during Hajj pilgrimage, including Acinetobacter baumannii with blaOXA-72, and Escherichia coli with blaNDM-5 carbapenemases – Thongpan Leangapichart – Antimicrobial Agents and Chemotherapy

Human gut microbiome

Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolome – Natalia Zeber-Lubecka –
Gut Microbes

Altered gut microbiota in Rett syndrome – Francesco Strati – Microbiome

Animal experiments

Honey bee gut microbiome is altered by in-hive pesticide exposures – Madhavi Kakumanu – Frontiers in Microbiology

Animal microbiome

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome – Hang Wang – The ISME Journal

Using the gut microbiota as a novel tool for examining colobine primate GI health – Katherine R. Amato – Global Ecology and Conservation

Plant, root, and soil microbiome

Bioprospecting metagenomics of a microbial community on cotton degradation: mining for new glycoside hydrolases – Guoxiu Zhang – Journal of Biotechnology

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain – Congcong Shen – Frontiers in Microbiology

Review: Plant litter decomposition: drivers insight to the ecological process – Gaurav Mishra – European Journal of Biological Research

Water and extremophile microbiome

Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes – Matthew T. Cottrell – Applied and Environmental Microbiology

Distribution and niche separation of planktonic microbial communities in the water columns from the surface to the hadal waters of the Japan Trench under the eutrophic ocean – Takuro Nunoura – Frontiers in Microbiology

Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area – Neng Fei Wang – Frontiers in Microbiology

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA – Priscilla J. Miranda – Frontiers in Microbiology

Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents – Begüm D. Topçuoğlu – Frontiers in Microbiology

Review: Halophiles: Champions of Environmental Adaptations and Their Industrial Applications – Rachana Singh – Current Biological Engineering (WTF: $63.00)

Review: An overview of siderophores for iron acquisition in microorganisms living in the extreme – Luis O. De Serrano – BioMetals

Air microbiome

Review: Approach of molecular methods for the detection and monitoring of microbial communities in bioaerosols: A review – Keunje Yoo – Journal of Environmental Sciences

Oil reservoir microbiome

Species divergence vs functional convergence characterizes crude oil microbial community assembly – Yong Nie – Frontiers in Microbiology

Metagenomics

Editorial: From Genes to Species: Novel Insights from Metagenomics – Eamonn P. Culligan – Frontiers in Microbiology

Sequencing techniques

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing – Minh Duc Cao – GigaScience

Microbes in the news

Poop Pill’s Surprise Failure Shows That the Microbiome is Still a Mystery – Ryan Cross – MIT Technology Review
Gut check: Seres Therapeutics shares plunge after microbiome drug fails in trial – CNBC
Seres Therapeutics Announces Interim Results from SER-109 Phase 2 ECOSPOR Study in Multiply Recurrent Clostridium Difficile Infection – Seres

I, microbe: Book Review of “I Contain Multitudes” by Ed Yong – Silvia Bulgheresi – Nature Microbiology
Hot off the press: Interview with Ed Yong – Andrew Jermy – Nature Microbiology

Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – EurekAlert
Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – Science Daily

Parasitic infection may have spoiled zebrafish experiments.Common contaminant may change shoaling behaviour, a proxy for stress and anxiety in behavioural studies. – Petra Szilagyi – Nature
What Does Your Poop Say About Your Evolution, and Other Ecological Connections to the Microbiome – Jens Hegg – PLOS Blogs

Powerful new bacteria discovered in Cookeville hot tub – Daily News Journal

Could a new CREAM fight off superbugs? Scientists develop lotion which stops bacteria getting into wounds – Madlen Davies – Daily Mail

There’s Nothing Green About Jill Stein’s Vaccine Stance – Emily Willingham – Forbes

Your soap and toothpaste could be messing with your microbiome – Alison Moodie – The Guardian

Anthrax sickens 13 in western Siberia, and a thawed-out reindeer corpse may be to blame – Ben Guarino – Washington Post

Bik’s not-microbiology Picks

Khloe Kardashian’s Vagina Oil Is a Bad Idea. Koko is telling her young female followers to moisturize their ‘vaginal lining’ with Vitamin E. Definitely do not do this– Samantha Allen – The Daily Beast

The Physicians Committee Releases Seven Dietary Guidelines for a Healthy Microbiota
The Key to Optimal Gut Health? Eat 50 to 55 Grams of Daily Fiber – PCRM

 

July 29, 2016

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Bifidobacteria/Spirochaetes trade-off in Italians vs. Hadza, asthma, transferring depression with human stool to rats, sea squirts symbionts, spacial structure of biofilms, and a glowing review of Ed Yong’s book “I Contain Multitudes”.

General microbiome

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients – Andrew Yeh – Shock

Pregnancy / human oral microbiome

Smoking, pregnancy and the subgingival microbiome – Akshay D. Paropkari – Scientific Reports

Review: An Integrated Review of Intestinal Microbiota in the Very Premature Infant – Melissa C. Dollings –  Neonatal Network

Human respiratory microbiome

Bacterial microbiota of the upper respiratory tract and childhood asthma – Martin Depner – Journal of Allergy and Clinical Immunology

Review: The role of anaerobic bacteria in the cystic fibrosis airway – Laura J. Sherrard – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Commentary: The relationship between the vaginal microbiome and human health – MR Millar – BJOG

Human gut microbiome

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome – Matteo Soverini – Frontiers in Microbiology

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations – Alessandra Riva – Environmental Microbiology

Histamine-secreting microbes are increased in the gut of adult asthma patients – Weronika Barcik – Journal of Allergy and Clinical Immunology

Dietary Supplementation with Rice Bran or Navy Bean Alters Gut Bacterial Metabolism in Colorectal Cancer Survivors – Amy M. Sheflin – Molecular Nutrition & Food Research

Four-week consumption of a Bifidobacterium bifidum strain modulates dominant intestinal bacterial taxa and fecal butyrate in healthy adults – Giorgio Gargari – Applied and Environmental Microbiology

Fecal microbiota transplantation for patients with steroid-resistant/dependent acute graft-versus-host disease of the gut – Kazuhiko Kakihana – Blood

Trial: Effect of prebiotic intake on gut microbiota, intestinal permeability and glycemic control in children with type 1 diabetes: study protocol for a randomized controlled trial – Josephine Ho – Trials

Opinion: How stable is the human gut microbiota? And why this question matters – Harald Brüssow – Environmental Microbiology

Research highlight: Microbial mobilomes differ between societies – Naomi Attar – Nature Reviews Microbiology

Review: High-Resolution Characterization of the Human Microbiome – Cecilia Noecker – Translational Research

Review: Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases – Mingming Sun – Journal of Gastroenterology

Review: The influence of gut derived CD39 regulatory T cells in CNS demyelinating disease – Javier Ochoa-Repáraz – Translational Research

Review: Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail – B Pigneur – Mucosal Immunology

Review: The Gut Microbiota in Immune-Mediated Inflammatory Diseases – Jessica D. Forbes – Frontiers in Microbiology

Review: Regulation of Autoimmunity by the Microbiome – Carlos R. Zárate-Bladés – DNA and Cell Biology

Animal experiments

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat – John R. Kelly – Journal of Psychiatric Research

The microbiota contributes to CD8+ T cell activation and nutrient malabsorption following intestinal infection with Giardia – Infection and Immunity – Aleksander Keselman

Gut Microbial Membership Modulates CD4 T Cell Reconstitution and Function after Sepsis – Javier Cabrera-Perez – Journal of Immunology

Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior – Caleb N. Fischer – bioRxiv

Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets – Lijuan Su – Applied Biochemistry and Biotechnology

Animal microbiome

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts – Lars Schreiber – Frontiers in Microbiology

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

Death Becomes Them: Bacterial community dynamics and stilbene antibiotic production in Galleria mellonella cadavers killed by Heterorhabditis/Photorhabdus – Amanda C. Wollenberg – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium – German Zafra – Journal of Hazardous Materials

Water and extremophile microbiome

Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale – Amit Vikram – Microbial Ecology

Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods – Vinh D. Pham – Environmental Microbiology

Protocol: Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME – Matthieu Leray – Marine Genomics

Protocol: Sampling of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication – Katja Lehmann – Marine Genomics

Microbes in space

Assessment of the Forward Contamination Risk of Mars by Clean Room Isolates from Space-Craft Assembly Facilities through Aeolian Transport – a Model Study – Luc van Heereveld – Origins of Life and Evolution of Biospheres

Built environment microbiome

Figures appear to show a gradual change, not a break, but: Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota – Cesira Giordano – Scientific Reports

Food microbiology

Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions – Cristian Bortolini – International Journal of Food Microbiology

Bioinformatics and metagenomics

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets – Scott C. Ritchie – Cell Systems

Techniques

The effect of DNA extraction methodology on gut microbiota research applications – Konstantinos Gerasimidis – BMC Research Notes

Biofilms

Review: Spatial structure, cooperation and competition in biofilms – Carey D. Nadell – Nature Reviews Microbiology

Microbes in the news

A glowing book review: Living in a microbial world, book review of “I Contain Multitudes The Microbes Within Us and a Grander View of Life” by Ed Yong – Susan Perkins – Science

State College of Florida, New College graduate wins microbiology award: Stephanie Morgan’s research won an award at the Small World Initiative Symposium – Bradenton Herald

Microbiology: A budding researcher creates a stir with her LIST-supported project: Camilla Hurst – Luxembourg Institute of Science And Technology (LIST)

‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – Harvard

‘Nose-y’ Bacteria Could Yield A New Way To Fight Infection – Carolyn Beans – NPR

The Marine Microbiome – A treasure trove of scientific and industrial potential – Cordis Europa
Video: Revealing the Secrets of Marine Microbes: methods that are being used to isolate and culture marine microorganisms – MaCuMBA project

July 28, 2016

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Maternal HIV status and infant microbiome development, nose bacteria producing antibiotics, gases produced by gut microbes, microbial mats in Hawaiian lava caves.

Pregnancy and birth

Maternal HIV infection influences the microbiome of HIV-uninfected infants – Jeffrey M. Bender – Science Translational Medicine

Press: Maternal HIV status may disrupt normal microbiome development in uninfected infants – Medical Xpress

Human respiratory microbiome

Human commensals producing a novel antibiotic impair pathogen colonization – Alexander Zipperer – Nature

Press: Scientists are looking everywhere, and we mean everywhere, for new antibiotics – Katherine Ellen Foley – Quartz
Nose-Dwelling Bacteria Could Be Antibiotic Factories, Study Says – Robert Lee Hotz – Wall Street Journal

Human vaginal microbiome

Desialylation of Neisseria gonorrhoeae Lipooligosaccharide by Cervicovaginal Microbiome Sialidases: The Potential for Enhancing Infectivity in Men – Margaret R. Ketterer – Journal of Infectious Diseases

Does the cervicovaginal microbiome facilitate transmission of Neisseria gonorrhoeae from women to men? Implications for understanding transmission of gonorrhea and advancing vaccine development – William M. Shafer – Journal of Infectious Diseases

Human gut microbiome

Review: Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota –  Alexander V. Oleskin – Microbial Ecology in Health and Disease

Press: Explosive new findings: Farting shown to play a role in regulating your brain and behavior – Kelly Hodgkins – Yahoo Tech

Review: Progress in Our Understanding of the Gut Microbiome: Implications for the Clinician – Sara Iqbal – Current Gastroenterology Reports

 
Animal microbiome

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows – Camilo Escallón – Functional Ecology

Review: The rich somatic life of Wolbachia – Jose E. Pietri – MicrobiologyOpen

Plant, root, and soil microbiome

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand – Laetitia Herrmann – Mycorrhiza

Bromeliad tanks are unique habitats for microbial communities involved in methane turnover – Franziska B. Brandt – Plant and Soil

Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota – Shazia N. Aslam – Environmental Microbiology

Assessing Fungal Population in Soil Planted with Cry1Ac and CPTI Transgenic Cotton and Its Conventional Parental Line Using 18S and ITS rDNA Sequences over Four Seasons – Xiemin Qi – Frontiers in Plant Science

Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization – Daniel B. Müller – Molecular and Cellular Proteomics

Water and extremophile microbiome

(PDF) Microbial mat communities in Hawaiian lava caves – Michael N. Spilde – International Symposium on Vulcanospeleology

Poster, abstract only: Microbial Diversity of Culinary Salts – Galen Muske – Utah Space Grant Consortium

Built environment microbiome

Influence of carbon sources and concrete on microbially induced corrosion of carbon steel in subterranean groundwater environment – Pauliina Rajala – Corrosion

Bioinformatics and metagenomics

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects – Wang Ying – OMICS: A Journal of Integrative Biology

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations – Aaron Y. Lee – BMC Bioinformatics

Review: Computational Biology in the 21st Century: Scaling with Compressive Algorithms – Bonnie Berger – Communications of the ACM

Microbes in the news

Five new studies will examine how the trillions of tiny organisms that call our bodies home can impact health – University at Buffalo

NASA releases ‘Microbiomics: The Living World In and On You’ – Video highlights Twins Study microbiome investigation – EurekAlert

The Olympians can leave. Brazil’s poor live with filthy, reeking water every day – Melissa Bailey – STAT News

Bizarre bacteria causing major cattle disease named by researchers – Pajaroellobacter abortibovis causes “foothill abortion disease” –  Science Daily

Bik’s non-microbiology Picks

From Impossible Foods, co-founded by Patrick Brown, a former Stanford professor: Impossible burger: New York’s latest food craze is a veggie burger that bleeds – Amanda Holpuch – The Guardian

July 24, 2016

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Songbird, soil nitrogen-cycling around the world, and parasites on an ancient butt-wipe stick.

Pregnancy and birth

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema – Heping Wang – Gut Pathogens

Human oral microbiome

Review: From focal sepsis to periodontal medicine: A century of exploring the role of the oral microbiome in systemic disease – Purnima S Kumar – The Journal of Physiology

Human gut microbiome

Review: The Role of the Gut Microbiome on Chronic Kidney Disease – B. Sampaio-Maia – Advances in Applied Microbiology

Review: The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health – Christopher A. Lowry – Current Environmental Health Reports

Animal and other experiments

Insulin resistance, microbiota and fat distribution changes by a new model of vertical sleeve gastrectomy in obese rats – Nicola Basso – Diabetes

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas – Katia Asmani – Aquaculture

Changes in the structure of the microbial community associated with Nannochloropsis salina following treatments with antibiotics and bioactive compounds – Haifeng Geng – Frontiers in Microbiology

Animal microbiome
Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird – Danielle J. Whittaker – Frontiers in Ecology and Evolution

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife – Maxime Galan – mSystems

Plant, root, and soil microbiome

Global biogeography of microbial nitrogen-cycling traits in soil – Michaeline B. Nelson – PNAS

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient – David J Eldridge – Journal of Animal Ecology

Biogeochemical drivers of microbial community convergence across actively retreating glaciers – Sarah C. Castle – Soil Biology and Biochemistry

The structure of bacterial communities along two vertical profiles of a deep colluvial soil – Marketa Sagova-Mareckova – Soil Biology and Biochemistry

Silver nanoparticles, ions and shape governing soil microbial functional diversity: nano shapes micro – Yujia Zhai – Frontiers in Microbiology

Water microbiome

Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks – Mariana P. Reis – Chemosphere

Effects of Copper, Nickel, and Sulphate from the Smelters at Sudbury, Ontario (Canada) on Microbial Communities in Lakes – Togwell A. Jackson – Geomicrobiology Journal

Archeological microbes

Early evidence for travel with infectious diseases along the Silk Road: Intestinal parasites from 2000 year-old personal hygiene sticks in a latrine at Xuanquanzhi Relay Station in China – Hui-Yuan Yeh – Journal of Archaeological Science: Reports

Press: Ancient Faeces Provide Earliest Evidence of Infectious Disease Being Carried on Silk Road – SciCasts
Ancient bottom wipers yield evidence of diseases carried along the Silk Road – Maev Kennedy – The Guardian

Built environment microbiome

Microorganisms associated with corrosion of structural steel in diverse atmospheres – Laura L. Machuca – International Biodeterioration & Biodegradation

More microbes

Individuals hospitalized with acute mania have increased exposure to antimicrobial medications – Robert Yolken – Bipolar Disorders

Metagenomics and bioinformatics

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents – Michael R. Wilson – mSystems

Microbes in the news

Everyday chemicals may be messing up our microbiomes—but we don’t know – Beth Mole – Ars Technica
The jury is still out on whether antibacterial chemical impacts microbiome or causes resistance – Bob Yirka – Medical Xpress

Some Microbes Have Been With Us Since Before We Existed. Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own. – Ed Yong – The Atlantic

Plants have a microbiome just like humans — and it could transform how our food is produced – Ariel Schwartz – Tech Insider

New book: The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life – Rodney Dietert
Your Microbes, Yourself. In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: – Louise Fabiani – Pacific Standard

Science, publishing, and career

The Women and the Science
Rachel Ignotofsky tells the stories of 50 women in science in her fantastic new science art book – Scientific American
Women in Science: An Illustrated Who’s Who – Julie Leibach – Science Friday

Women in Science: An Illustrated Who’s Who

July 22, 2016

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Fungi in human GI tract, antibiotics reduce Alzheimer’s lesions in mouse model, cospeciation of primates and gut microbes, dangerous bacteria after sewer spill.

Jobs

Research scientists to engineer microbiome engineering therapies – Eligo Bioscience

General microbiome

Perspective: Is triclosan harming your microbiome? – Alyson L. Yee – Science

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

Pregnancy and birth microbiome

Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term – Akila Subramaniam – American Journal of Perinatology

Human mouth microbiome

Salivary and fecal microbiota and metabolome of celiac children under gluten-free diet – Maria De Angelis – International Journal of Food Microbiology

Human respiratory microbiome

Lung Microbiome in HIV Infection – Homer L. Twigg III – Translational Research

Human vaginal microbiome

Proceedings of the 2015 NIH/NIAID Bacterial Vaginosis Expert Consultation – The Journal of Infectious Diseases

Human gut microbiome

Age and gender affect the composition of fungal population of the human gastrointestinal tract – Francesco Strati – Frontiers in Microbiology

A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression – Shuanghong Jiang – Antonie van Leeuwenhoek

Review: An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome – Carl E. Cerniglia – Drug Testing and Analysis

Animal experiments

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Press: Antibiotics weaken Alzheimer’s disease progression through changes in the gut microbiome – EurekAlert
Could antibiotics reduce levels of Alzheimer’s-causing plaques? – Hannah Nichols – MedicalNewsToday

Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38 – Christopher P Arnold – eLIFE

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system – Emilie Cardona – BMC Microbiology

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota – Isabella M. Cattadori – PLOS ONE

Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota – Sophie Yurist-Doutsch – PLOS ONE

Celecoxib alters the intestinal microbiota and metabolome in association with reducing polyp burden – David C. Montrose – Cancer Prevention Research

Review: Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome – Siegfried Ussar – Molecular metabolism

Animal microbiome

Cospeciation of gut microbiota with hominids – Andrew H. Moeller – Science

Press: Primates, Gut Microbes Evolved Together. Symbiotic gut bacteria evolved and diverged along with ape and human lineages, researchers find – Anna Azvolinsky – The Scientist
Microbes in our guts have been with us for millions of years – Ann Gibbons – Science
Your gut bacteria predates appearance of humans, genetic study finds – Naomi Stewart – The Guardian

A snapshot of the microbiome of Amblyomma tuberculatum ticks infesting the gopher tortoise, an endangered species – Khemraj Budachetri – Ticks and Tick-borne Diseases

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? –
Antton Alberdi – Trends in Ecology & Evolution

Vaginal microbial communities from synchronized-heifers and cows with reproductive disorders – Candelaria Gonzalez Moreno – Journal of Applied Microbiology

Review: The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins – Kevin D. Kohl – Frontiers in Microbiology

Plant, root, and soil microbiome

Plant Identity Exerts Stronger Effect than Fertilization on Soil Arbuscular Mycorrhizal Fungi in a Sown Pasture – Yong Zheng – Microbial Ecology

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra – Mallappa Manjunath – Heliyon

Naming Potentially Endangered Parasites: Foliicolous Mycobiota of Dimorphandra wilsonii, a Highly Threatened Brazilian Tree Species– Meiriele da Silva – PLOS ONE

Contribution of the seed microbiome to weed management – D Müller-Stöver – Weed Research

Mycorrhizal associations of trees have different indirect effects on organic matter decomposition – Melanie K. Taylor – Journal of Ecology

Water and extremophile microbiome

Vancomycin resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment – Suzanne Young – Applied and Environmental Microbiology

Press: USF researchers find dangerous bacteria after sewer spills – EurekAlert
USF researchers say they found dangerous bacteria after sewage spill – Anne Lindberg – Saint Peters Blog

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers – Amandine Laffite – Frontiers in Microbiology

Microbial communities in sediments of Lagos Lagoon, Nigeria: Elucidation of community structure and potential impacts of contamination by municipal and industrial wastes – Chioma C. Obi – Frontiers in Microbiology

Cryoconite pans on Snowball Earth: supraglacial oases for Cryogenian eukaryotes? – P. F. Hoffman – Geobiology

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality – Fabian Roger – Ecology

Heterotrophic bacteria in Antarctic lacustrine and glacial environments – Johanna Laybourn-Parry – Polar Biology

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico) – M. Crespo-Medina – Geobiology

Bioinformatics and metagenomics

MetaG: a graph-based metagenomic gene analysis for big DNA data – Linkon Chowdhury – Network Modeling Analysis in Health Informatics and Bioinformatics

DFAST and DAGA: web-based integrated genome annotation tools and resources – Yasuhiro Tanizawa – Bioscience of Microbiota, Food and Health

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

Breast-feeding the Microbiome (Excerpt from his book) – Ed Yong – New Yorker

Janet Jansson Among Nine Authors of Nature Review Article – PNNL

Northern Arizona University professor Bruce Hungate named a fellow of the American Academy of Microbiology – Arizona Business Daily

UF scientists identify seal as source of new strain of bacteria that caused disease in hunter – Sarah Carey – University of Florida

Gut Bacteria May Drive Inflammation in Sepsis, ARDS – Salynn Boyles – MedPageToday

With Rob Knight as keynote speaker: Fermenting Knowledge at Fermentation Festivals (with Kombucha Recipe) – John D. Ivanko – Mother Earth News

Your death microbiome could catch your killer – Anna Williams – New Scientist

Microbes and money

Osel, Inc. Comments on New Study Showing Role of Vaginal Microbiome in Women’s Health – PharmiWeb

Q&A: Indigo’s CEO Reveals the Strategy Behind Its Plant Microbiome Technology – Olivia Vanni – BostInno

Eminent Harvard Geneticist Professor George Church Joins uBiome Advisory Board – Benzinga

Immuron to Cooperate with Leading Australian Universities on Autism Research – Nasdaq