Category Archives: Water microbiome

April 18, 2016

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Tongue coating and halitosis, mucosa and Crohn’s, biography in American forests diazotrophs, and microbes on parchment documents.

Events

Submit your microbial artwork and win the ISMEJ cover competition! – The ISME Journal

Human oral microbiome

Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis – Wen Re – Scientific Reports

Human respiratory microbiome

Clinical impact of methicillin-resistant staphylococcus aureus on bacterial pneumonia: cultivation and 16S ribosomal RNA gene analysis of bronchoalveolar lavage fluid – Toshinori Kawanami – BMC Infectious Diseases

Human gut microbiome

Mucosa-attached bacterial community in Crohn’s Disease coheres with the Clinical Disease Activity Index – Holger Schäffler – Environmental Microbiology Reports

Animal microbiome

Impact of gut microbiota on the fly’s germ line – Michael Elgart – Nature Communications

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Plant, root, and soil microbiome

Biogeographic Patterns of Soil Diazotrophic Communities across Six Forests in the North America – Qichao Tu – Molecular Ecology

Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil – Daniel I. Kaplan – Environ. Sci. Technol.

Water microbiology

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments – Elizabeth Trembath-Reichert – PeerJ

Air microbiology

Assessment of microbial communities in PM1 and PM10 of Urumqi during winter – Huange Gou – Environmental Pollution

Waste and pollution microbiology

Geochemical and temporal influences on the enrichment of acidophilic iron-oxidizing bacterial communities – Yizhi Sheng – Applied and Environmental Microbiology

Review: Insights into microbial diversity in wastewater treatment systems: How far have we come? – Isabel Ferrera – Biotechnology Advances

Built environment microbiology

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards – Tomasz Lech – Applied and Environmental Microbiology

Extraction of Aerosol-Deposited Yersinia pestis from Indoor Surfaces To Determine Bacterial Environmental Decay – Ian M. Gut- Applied and Environmental Microbiology

More microbiology

Mechanisms of Bacterial (Serratia marcescens) Attachment to, Migration along, and Killing of Fungal Hyphae – Tal Hover – Applied and Environmental Microbiology

Principles for designing synthetic microbial communities – Nathan I Johns – Current Opinion in Microbiology

Microbes and art

Bacteria Rule Everything Around Me – Geoff Manaugh – BLDG blog

‘Financial Growth’ reveals just how much coins and money can communicate, transfer and exchange – Heidi Hinder

Microbes in the news

In Dutch, with quotes from me: Ineens zit je wel en wee in je darm – Sander Voormolen – NRC

The Endurance of Microbiology: An Interview with Mike Jetten, Mark Martin, Ute Römling, and Victor Torres – Trends in Microbiology

‘We have never been this close’: The campaign to eradicate polio takes a giant step forward – Helen Branswell – STAT News

Antarctica research published – Mike Henson – Thrash Lab

Q&A with Councilor Eva Harris on battle against Zika – American Society of Tropical Medicine and Hygiene

Creating a biobank of the Flagstaff community: Me and my microbiota – Tom Carpenter – AZ Daily Sun

The Human Body’s Complicated Relationship With Fungi – Bret Stetka – WCQS

Queens University student discovers a virus strain – News Observer

Researchers chew over the differences in mouth bacteria in horses – HorseTalk

Newly discovered microbe keeps teeth healthy: Bacteria may offer a new way to prevent cavities – Society for Science

Next job for the microbiome: Tagging criminals – Andrew Porterfield – Genetic Literacy Project

Great Barrier Reef: the scale of bleaching has the most sober scientists worried – James Woodford – The Guardian

Viruses Find Love In A Boiling Place – Inside Science

UB establishes Center for Microbiome Research – University at Buffalo

Cow’s milk has vital prebiotic for a healthy baby’s microbiome – New Scientist

Mainstreaming the Microbiome – Susan K Finston – Biotech blog

Study: Jet Hand Dryers Blast Bacteria Around Bathrooms with Terrifying Force – Ed Jones – Modern Readers

April 13, 2016

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Thematic issue on effect of antibiotics on microbiomes, limited effect of probiotics on stool proteomics, culex mosquito development, ocean acidification, and new technique to determine microbial growth.

General microbiome

Thematic Issue: the effects of anthropogenic use of antibiotics on the microbiomes in various ecosystems and the implications for human health. Guest edited by Prof. Kornelia Smalla, the articles included in this issue are freely available to read til 11th May 2016. Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology
Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Editorial: Microbiome: Eating for trillions – Derrick M. Chu – Nature

Pregnancy and birth

Preview: Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites – Seth Rakoff-Nahoum – Cell Host & Microbe

Review: The interplay of host immunity and environment on risk for bacterial vaginosis and associated reproductive health outcomes – Kerry Murphy – The Journal of Infectious Diseases

Human respiratory microbiome

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype – Leopoldo N. Segal – Nature Microbiology

Human gut microbiome

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults – Carolin A. Kolmeder – PLOS ONE

Review: The gut microbiota and metabolic disease: current understanding and future perspectives – T. Arora – Journal of Internal Medicine

Animal models

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing – Anisa S. Ismail – Cell Host & Microbe

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella – Fabian Rivera-Chávez – Cell Host & Microbe

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations – Alexander R. Moschen – Cell Host & Microbe

Animal microbiome

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast – Leonardo M. Díaz-Nieto – PLOS ONE

Plant, root, and soil microbiome

Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient – Katja Steinauer – BMC Ecology

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus – Marta Alves – Scientific Reports

Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures – Yanfeng Cao – Applied Soil Ecology

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil – Samiran Banerjee – Soil Biology and Biochemistry

Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism – Nick Bouskill – Frontiers in Microbiology

Water and extremophile microbiome

Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary – Nachshon Siboni – Frontiers in Microbiology

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields – Thomas Rime – Soil Biology and Biochemistry

Implications of Ocean Acidification for Marine Microorganisms from the Free-Living to the Host-Associated – Paul A. O’Brien – Frontiers in Marine Science

Waste and pollution microbiology

Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater – Jia Liu – Journal of Environmental Sciences

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area – James F. Douglass – Journal of Soils and Sediments

The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation – Holger Schmidt – Freshwater Biology

Review: The importance of sewer biofilms – Henriette Jensen – Water

Food microbiology and functional foods

Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice – Yi-Ming Chen – MDPI Nutrients

Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis – Christophe Monnet – Frontiers in Microbiology

Review: Prebiotics as a modulator of gut microbiota in paediatric obesity – A. C. Nicolucci – Pediatric Obesity

Techniques

Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples – Egbert Schwartz – Current Opinion in Biotechnology

Review: A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis – Aditi Sengupta – Agricultural & Environmental Letters

Microbial ecology

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning – Manuel Delgado-Baquerizo

Influence of dormancy on microbial competition under intermittent substrate supply: Insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

More microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis – Matt S. Conover – mBio

Biostatistics

Reinventing Biostatistics Education for Basic Scientists – Tracey L. Weissgerber – PLOS Biology

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

SCSU prof Elizabeth Lewis Roberts discovers fungus, bacteria help grass (really) – Anna Bisaro – New Haven Register

Probiotics for Livestock – Reducing Antibiotic Reliance – Alex Alexiev – MicroBEnet

Taking Cues From Human Nutrition To Reduce Antibiotic Use In Livestock – Amy Mayer – NPR

Why bacteria can’t get any bigger—or smaller – Elizabeth Pennisi – Science

Digestion of lignin in the gut – Science Daily

“Truly exciting”: Probiotic may increase muscle mass, energy & performance – Stephen Daniells – Nutraingredients

Breakthrough at Binghamton furthers development of bacteria-powered energy – The Engineer

Vibrio: Aggressive infectious bacteria species found in Sydney Harbour – Daisy Dumas – Sydney Morning Herald

Science, publishing, and career

Do interventions to reduce misconduct actually work? Maybe not, says new report – Alison McCook – Retraction Watch

$250 million, 300 scientists and 40 labs: Sean Parker’s revolutionary project to ‘solve’ cancer – Ariana Eunjung Cha – Washington Post

Science fairs are as flawed as my solar-powered hot dog cooker – Carl Zimmer – STATnews

The dark side of Guardian comments: part of a series on the rising global phenomenon of online harassment – the Guardian

How one lab challenged a grant rejection and won €5 million – Ewen Callaway – Nature

April 12, 2016, the late one

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Events

Standards for Microbiome Measurements Workshop – August 9-10, NIST, Gaithersburg, Md

General microbiome

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Moving microbiota research towards establishing causal associations that represent viable targets for effective public health interventions – Volker Mai – Annals of Epidemiology

Evolution of Koch’s postulates: towards a twenty-first century understanding of microbial infection – Guido Antonelli – Clinical Microbiology and Infection

Thematic Issue: Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology

Human oral microbiome

http://www.sciencedirect.com/science/article/pii/S104727971630076XThe Effects of Family, Dentition and Dental Caries on the Salivary Microbiome – Betsy Foxman – Annals of Epidemiology

Red fluorescent biofilm: the thick, the old, and the cariogenic – Catherine M.C. Volgenant – Journal of Oral Microbiology

Human gut microbiome

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening – Nielson T Baxter – BioRxiv Preprint

Changes in Korean Adult Females’ Intestinal Microbiota Resulting from Kimchi Intake – Kim JY – Omics Journal of Nutrition & Food Sciences

Review: The Fiber Gap and the Disappearing Gut Microbiome: Implications for Human Nutrition – Edward C. Deehan – Trends in Endocrinology & Metabolism

Animal model microbiome

Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism – P Zheng – Molecular Psychiatry

Temperate phages enhance pathogen fitness in chronic lung infection – Emily V Davies – The ISME Journal

Bacteraemia before during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal

Animal microbiome

Population and individual level dynamics of intestinal microbiota of a small primate – Tuomas Aivelo – Applied and Environmental Microbiology

The nasopharyngeal microbiota in feedlot cattle and its role in respiratory health – Edouard Timsit – Animal Frontiers

Review: Gut microbiome and omics: a new definition to ruminant production and health – Nilusha Malmuthuge – Animal Frontiers

Plant, root, and soil microbiome

Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass – Lin Chen – Soil Biology and Biochemistry

Assessing microbial activities in metal contaminated agricultural volcanic soils – An integrative approach – C. Parelho – Ecotoxicology and Environmental Safety

Review: The role of locally adapted mycorrhizas and rhizobacteria in plant-soil feedback systems – Daniel Revillini – Functional Ecology

Water microbiome

Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone – Claudia Lüke – PeerJ

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms – Hanno Teeling

Transporting Ocean Viromes: Invasion of the Aquatic Biosphere – Yiseul Kim – PLOS ONE

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing – Marija Kaevska – SpringerPlus

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets – Lukáš Falteisek – Microbial Ecology

Bioinformatics and metagenomics

Chapter: Improving Bloom Filter Performance on Sequence Data Using kk-mer Bloom Filters – David Pellow – Research in Computational Molecular Biology

Microbial ecology

A Game Theoretical Approach to Microbial Coexistence – Monica Abrudan – Advances in Dynamic and Evolutionary Games

The ecologist’s field guide to sequence-based identification of biodiversity –
Simon Creer – Methods in Ecology and Evolution

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

Mind the fibre gap: The case of the vanishing gut microbiome – Will Chu – NutraIngredients

uBiome Opens Voting to all Citizen Scientists to Select $100k Microbiome Research Grant Winner – uBiome

Here’s the mounting evidence against using antibacterial soaps; Few pros, but cons include upped risk of infection, microbiome changes, drug resistance – Beth Mole – Ars Technica

Six-step hand-washing technique most effective for reducing bacteria in hospitals – Glasgow Chamber of Commerce

Hacking Gut Bacteria Could Be The Future Of Medicine. MIT biologists are reprogramming gut bacteria as “live therapeutics.” – Carolyn Gregoire – Huffington Post

Feeding Bacteria to Livestock Could Cut Antibiotic Use – Amy Mayer – Iowa Public Radio

Drug-resistant bacteria found scattered in soil – V. Nilesh – Deccan Chronicle

Sweet Siren call of surface lures bacteria to their death – Anthony King – Chemistry World

New Tree of Life Beautifully Illustrates the Enormous World of Bacteria – Kate Horowitz – Mental Floss

April 12, 2016, part 1

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Too many alerts to go through after taking one day off, so here is part one. An updated tree of life, acute appendicitis, rhizosphere of a living fossil plant, Antarctic surface snow, and effects of Superstorm Sandy on creek water.

Jobs and events

Senior Scientist with significant track record in microbiome research – The National Institute for Biological Standards and Control, South Mimms, UK

General microbiome

A new view of the tree of life – Laura A. Hug – Nature Microbiology

Pregnancy and birth

The Gestational Vaginal Microbiome and Spontaneous Preterm Birth among Nulliparous African American Women – Deborah B. Nelson – American Journal of Perinatology

Early colonization of functional groups of microbes in the infant gut – Van T. Pham – Environmental Microbiology

The gut resistome is highly dynamic during the first months of life – Christian JH von Wintersdorff – Future Medicine

Human skin microbiome

Review: Skin Biomes – N. Fyhrquist – Current Allergy and Asthma Reports

Human respiratory microbiome

Review: Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis – A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions – Jake Jervis Bardy – Ann Otol Rhinol Laryngol

Human oral microbiome

The salivary microbiome for differentiating individuals: proof of principle – Sarah L. Leake – Microbes and Infection

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples – Jean-Luc C. Mougeot – Journal of Oral Microbiology

Human gut microbiome

There are no Enterotypes: Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome

Experiment with n=1: Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota – Blanca S. Noriega – Case Reports in Medicine

First Occurrence of Severe Extraintestinal Manifestations of Crohn’s Disease Following Faecal Microbiota Transplantation – Niels Teich – Journal of Crohn’s and Colitis

Acute appendicitis in children is associated with a local expansion of Fusobacteria – Matthew B. Rogers – Clinical Infectious Diseases

Hypothesis: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? – Alexis Mosca – Frontiers in Microbiology

Not endorsing, because highly controversial and not well founded: Bread and Other Edible Agents of Mental Disease – Paola Bressan and Peter Kramer – Frontiers in Human Neuroscience

Review: The human gut microbiome in health: establishment and resilience of microbiota over a lifetime – Kacy Greenhalgh – Environmental Microbiology

Review: Cytotoxicity of Nanoparticles Contained in Food on Intestinal Cells and the Gut Microbiota – Esther E. Fröhlich – MDPI International Journal of Molecular Sciences

Review: The Role of the Gut Microbiota in Childhood Obesity – Pihl Andreas Friis – Childhood Obesity

Animal models

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions – Rebeca Martín – Frontiers in Microbiology

Depletion of Cultivatable Gut Microbiota by Broad-Spectrum Antibiotic Pretreatment Worsens Outcome After Murine Stroke – Katarzyna Winek – Stroke

Plant, root, and soil microbiome

Common mycorrhizal networks and their effect on the bargaining power of the fungal partner in the arbuscular mycorrhizal symbiosis – Heike Bückinga – Communicative & Integrative Biology

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific – Catarina Cúcio – Frontiers in Microbiology

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil – Angel Valverde – PLOS ONE

Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents – Antonio Gazol – FEMS Microbiology Ecology

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms – Samir Rezki – PeerJ

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function – Jennifer E. Schmidt – Frontiers in Plant Science

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima – Daniel F R Cleary – Plant Biology

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists – Stefan Geisen – Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status – Yuyin Yang – Frontiers in Microbiology

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow – Anna Lopatina – Frontiers in Microbiology

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Impact of an intense water column mixing (0-1500m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea – T. Severin – Environmental Microbiology

Aquatic bacterial community is restructured by hydric dynamics associated with Superstorm Sandy – Nikea Ulrich – Applied and Environmental Microbiology

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula – Daniel Aguirre de Cárcer – FEMS Microbiology Ecology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Partitioning of Viruses in Wastewater Systems and Potential for Aerosolization – Mari Titcombe Lee – Environmental Science & Technology Letters

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow – Serena Caucci – FEMS Microbiology Ecology

Spatial and temporal variability of bacterial communities within a combined sewer system – Henriette Stokbro Jensen – MicrobiologyOpen

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters – Rasmus Hansen Kirkegaard – The ISME Journal

Bioinformatics

Not endorsing: Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification – Yin Wang – BioMed Research International

More microbiology

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo – Nathan D. McDonald – mBio

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota – Si Ming Man – Pathogens and Disease

Microbes in the news

Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there – Ed Yong – The Atlantic

Wealth of unsuspected new microbes expands tree of life – Science Daily

Can more fiber restore microbiome diversity? – Science Daily

Science, publishing, and career

Research Funding: the Case for a Modified Lottery – Ferric C. Fang and Arturo Casadevall – mBio

 

April 7, 2016

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Biases and challenges with microbiome data, metabolic syndrome, stem cell transplants, ammonia-eating bacteria in fish gills, and a distinct pilus in the gut microbiome.

Events

Webinar: Cancer and the Oral Microbiome: A Metagenomics Approach – Scott Kelley, April 25

General microbiome

Good read about biases: Commentary: Challenges for Case-Control Studies with Microbiome Data – J. Paul Brooks – Annals of Epidemiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Perspective: Microbiome and Anticancer Immunosurveillance – Laurence Zitvogel – Cell

Human oral microbiome

Effects of triclosan on host response and microbial biomarkers during experimental gingivitis – Brooke A. Pancer – Journal of Clinical Periodontology

Human skin microbiome

Review: New insights into acne pathogenesis: Exploring the role of acne-associated microbial populations – Bipul Kumar – Dermatologica Sinica

Human respiratory microbiome

Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota – Jonathan M. Mansbach – Journal of Allergy and Clinical Immunology

Review: The respiratory microbiome: An underappreciated player in the human response to inhaled pollutants? – Sara D. Adar – Annals of Epidemiology

Human gut microbiome

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Mi Young Lim – Gut

Functional changes in gut microbiota during haematopoietic stem cell transplantation for severe combined immunodeficiency – Jonathan P. Lane – Journal of Allergy and Clinical Immunology

Interplay between bile acid metabolism and microbiota in irritable bowel syndrome – M. Dior – Neurogastroenterology & Motility

Review: The Intestinal Microbiota in Metabolic Disease – Anni Woting – MDPI Nutrients

Animal models

The absence of microbiota delays the inflammatory response to Cryptococcus gattii – Marliete Carvalho Costa – International Journal of Medical Microbiology

Brain injury induces specific changes in the caecal microbiota of mice via altered autonomic activity and mucoprotein production – A. Houlden – Brain, Behavior, and Immunity

Animal microbiome

Branchial nitrogen cycle symbionts can remove ammonia in fish gills – Maartje A.H.J. van Kessel – Environmental Microbiology Reports

Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis – Helene Falentin – Frontiers in Microbiology

Plant, root, and soil microbiome

Could The Martian science heck work? Evolution of soil on Mars – Shannon Bohle – Astronomy & Geophysics

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Amplicon-based metabarcoding reveals temporal response of soil microbial community to fumigation-derived products – Feng Wei – Applied Soil Ecology

Water microbiome

Identification of bacterial communities in sediments of Poyang Lake, the largest freshwater lake in China – Wenbo Kou – SpringerPlus

Influence of selected environmental factors on the abundance of aerobic anoxygenic phototrophs in peat-bog lakes – Sylwia Lew – Environmental Science and Pollution Research

Other microbiology

From Bacteroidia: A Distinct Type of Pilus from the Human Microbiome – Qingping Xu – Cell

Identification of new drug candidates against Borrelia burgdorferi using high-throughput screening – Venkata Raveendra Pothineni – Drug Design, Development and Therapy

Microbes and art

Another report on this beautiful art: Microbiome Art by Joana Ricou – Alex Alexiev – MicroBEnet

Students paint bacteria in cross campus learning Science Meets Art is a part of the SciCom initiative which is intended to help science students communicate their work and research – Connie Beltran – Texas Christian University

Microbes in the news

“Evolution of Soil on Mars”… where fiction becomes fact – David Coil – MicroBEnet

Gut Microbiota Altered in First-Episode Schizophrenia – Liam Davenport – Medscape

Gut Microbiome May Play Role in Myelination Disorders Including Multiple Sclerosis – interview with John Cryan – Medical Research

New type of symbiosis: Bacteria eat ammonia in fish gills – Science Daily

Elucidating the Microbiome of Acne Pathogenesis – Clincical Microbiomics

Biofilm oscillations: Excellent Paper on Metabolism dynamics + a video – Ben Libberton – NPJ Biofilms Community

California Strains of Lyme Bacteria May Survive Antibiotic Treatment According to Study – PR NewsWire

 

April 6, 2016

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C-section and gut colonization, N. flavescens in celiac patients, Lactobacillus in the gut, bird or whiskey, bacteria attached to phytodetritus, microbiology in the classroom, and CRISPR to decipher and shape bacterial diversity. And a bad article about women in space.

Event

Microbiome: How Commensal Bacteria Can Be Our Friends – A Talk by Dr. Deepshika Ramanan – April 14, Genspace Brooklyn, NY, Genspace

Organizing 2017 Microbes of the Built Environment conference, call for community input – Lynn Schriml – MicroBEnet

Pregnancy and birth

Cesarean section changes neonatal gut colonization – Jakob Stokholm – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Bacterial–viral load and the immune response in stable and exacerbated COPD: significance and therapeutic prospects – Silvestro Ennio D’Anna – International Journal of Chronic Obstructive Pulmonary Disease

Human gut microbiome

Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients – Valeria D’Argenio – American Journal of Gastroenterology

Th17 responses and natural IgM antibodies are related to gut microbiota composition in systemic lupus erythematosus patients – Patricia López – Scientific Reports

Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota – Maddalena Rossi – Environmental Microbiology Reports

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children – Guojun Wu – Scientific Reports

DGGE: The Effect of Probiotic Treatment on Patients Infected with the H7N9 Influenza Virus – Xinjun Hu – PLOS ONE

Review: Use your antibiotics wisely. Consequences to the intestinal microbiome – Jorge Cervantes – FEMS Microbiology Letters

Review: Diet, Microbiota, Obesity, and NAFLD: A Dangerous Quartet – Mariana Verdelho Machado – MDPI International Journal of Molecular Sciences

Animal models

Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency – Bradley W. Richmond – Nature Communications

Reproduction and Growth in a Murine Model of Early Life-Onset Inflammatory Bowel Disease – Eniko Nagy – PLOS ONE

Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces – Yingying Zhu – PLOS ONE

Colitis susceptibility in p47 phox−/− mice is mediated by the microbiome – E. Liana Falcone – Microbiome

Review: Multiscale analysis of the murine intestine for modeling human diseases – Jesse Lyons – Integrative Biology

Animal microbiome

The bird, not the whiskey: Activity of urealytic microorganisms in the gastrointestinal tract of the black grouse Lyrurus tetrix – M. V. Vecherskii – Doklady Biological Sciences

Plant, root, and soil microbiome

Zinc treatment increases the titre of ‘Candidatus Liberibacter asiaticus’ in huanglongbing-affected citrus plants while affecting the bacterial microbiomes – M.Q. Zhang – Journal of Applied Microbiology

Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata – Christophe Vieira – Frontiers in Microbiology

Water and extremophile microbiome

Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria – Margaret Findlay – Environmental Science & Technology

Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China – Lei Zhang – Canadian Journal of Microbiology

Dynamic of bacterial communities attached to lightened phytodetritus – Morgan Petit – Environmental Science and Pollution Research

Waste and pollution microbiology

Detection of the Antimicrobial Triclosan in Environmental Samples by Immunoassay – Ki Chang Ahn – Environmental Science & Technology

Lactic acid fermentation from food waste with indigenous microbiota: Effects of pH, temperature and high OLR – Jialing Tang – Waste Management

Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations – Sevcan Aydin – Bioresource Technology

Microbial Ecology

Host behaviour–parasite feedback: an essential link between animal behaviour and disease ecology – Vanessa O. Ezenwa – Proceedings of the Royal Society B

Myxococcus xanthus: Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

Review: Deciphering and shaping bacterial diversity through CRISPR – Alexandra E Briner – Current Opinion in Microbiology

Microbes and education

Nice set of papers in ASM’s Journal of Microbiology and Biology Education:

Microbes in the news

The Scary Thing About a Virus That Kills Farmed Fish – Ed Yong – The Atlantic

Seres Therapeutics: All You Need To Know About What Will Be The First Prescription Microbiome Company – Seeking Alpha

Type IV pili: Appendages Help Microbes Survive Harsh Conditions – Charles Q. Choi – Astrobiology

Not endorsing this article. Microbiotas of men and women are not that different, not much published data on effects of space flight on gut microbiome, and I did not like the suggestion that women will get sick more often. Also, antibiotics ain’t gonna help if women have breast cancer.
Gender generates biological challenges for long duration spaceflight – Evan Gough

So long lithium, hello bacteria batteries? – ScienMag (not to be confused with Science)

Microbes in the news

Targeting the gut microbiome to fight heart disease – American Society for Microbiology

Science, publishing, and career

The Immoral Landscape? Scientists Are Associated with Violations of Morality – Bastiaan T. Rutjens – PLOS ONE

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

April 4, 2016

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Gut microbiome of Australian sea lions, Trichoderma fungi in endemic plants, and digging for microbial proof of Hannibal’s route over the alps.

Human vaginal microbiome

Comment: Translating the vaginal microbiome: gaps and challenges – Jacques Ravel – Genome Medicine

Human respiratory microbiome

Review: The lung microbiome: the perfect culprit for COPD exacerbations? – Carine Gomez – European Respiratory Journal

Animal models

Frogs: Short-term exposure to coal combustion waste has little impact on the skin microbiome of adult spring peepers, Pseudacris crucifer – Myra C. Hughey – Applied and Environmental Microbiology

Short bowel syndrome (SBS)-associated alterations within the gut-liver axis evolve early and persist long-term in the piglet model of short bowel syndrome – Prue M. Pereira-Fantini – Journal of Gastroenterology and Hepatology

Maternal Antibiotic Treatment Impacts Development of the Neonatal Intestinal Microbiome and Antiviral Immunity – Gabriela Gonzalez-Perez – The Journal of Immunology

Generation and Characterization of Indoor Fungal Aerosols for Inhalation Studies – Anne Mette Madsen – Applied and Environmental Microbiology

Correspondence: The premature invocation of a ‘gut-lung axis’ may obscure the direct effects of respiratory microbiota on pneumonia susceptibility – Robert P Dickson – Gut

Animal microbiome

Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea) – Tiffany C. Delport – Applied and Environmental Microbiology

DGGE: Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca) – Zhirong Peng – World Journal of Microbiology and Biotechnology

Germs within Worms: Localization of Neorickettsia sp. within Life Cycle Stages of the Digenean Plagiorchis elegans – Stephen E. Greiman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes – Jinping Zhang – World Journal of Microbiology and Biotechnology

Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens – Christin Zachow – Journal of Biotechnology

Water microbiome

Diverse and temporally-variable particle-associated microbial communities are insensitive to bulk seawater environmental parameters – Cheuk-Man Yung – Applied and Environmental Microbiology

Pollution and waste microbiology

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments – Emine Ertekin – Environmental Science & Technology

Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons – Benjamin D. Folwell – Applied and Environmental Microbiology

Microbes and art

These petri dish “paintings” reveal the hidden beauty of bacteria – Julia Belluz – Vox

After Effects: A series of architectural scale models constructed with black paper and covered with flour and a layer of mould to create the effect of old abandoned buildings – Daniele Del Nero.

Microbes in the news

Scarlett Fever: A 19th-century disease is on the rise in the UK—and nobody knows why – Akshat Rathi – Quartz

The truth about Hannibal’s route across the Alps. How exactly did the Carthaginian general and his elephants reach Italy? Scientists have got their hands dirty to come up with an answer – Philip Ball – The Guardian

Gender differences in antibiotic prescribing in the community: a systematic review and meta-analysis – Wiebke Schröder – Journal of Antimicrobial Chemotherapy

Microbes Meet Cancer. Understanding cancer’s relationship with the human microbiome could transform immune-modulating therapies – Kate Yandell – The Scientist

Guts and Glory. An open mind and collaborative spirit have taken Hans Clevers on a journey from medicine to developmental biology, gastroenterology, cancer, and stem cells – Anna Azvolinsky – The Scientist

Science, pubilishing, and career

Medscape Physician Compensation Report 2016 – Carol Peckham – MedScape

Bik’s Picks

It turns out this planet has three suns in its sky – Rachel Feltman – Washington Post

April 2, 2016

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Yes, it is technically already April 3, but I only got to do the daily roundup late tonight, so I did not quite get it done in time. C-section and weight influence on infant colonization, dachshunds, crops selecting fungi, post-mortem microbial transmigration

Pregnancy and birth

Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome – Noel T. Mueller – Scientific Reports

Study provides evidence that “vaginal seeding” of infants born by caesarean partially restores microbiota – Amali Lokugamage – BMJ

Relationship between milk microbiota, bacterial load, macronutrients and human cells during lactation – Alba Boix-Amoros – Frontiers in Microbiology

Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization – David E. Brumbaugh – Journal of Pediatric Gastroenterology & Nutrition

Effect of Formula Containing Lactobacillus Reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section – Rodenas, Clara L. Garcia – Journal of Pediatric Gastroenterology & Nutrition

Human oral microbiome

Mucosal and salivary microbiota associated with recurrent aphthous stomatitis – Yun-ji Kim- BMC Microbiology

Assessment of oral malodor and tonsillar microbiota after gargling with benzethonium chloride – Yuki Iwamura – Journal of Oral Science

Potential screening and early diagnosis method for cancer: Tongue diagnosis – Shuwen Han – International Journal of Oncology

In vitro: A dual-species microbial model for studying the dynamics between oral streptococci and periodontal pathogens during biofilm development on titanium surfaces by flow cytometry – Anita Manti – Research in Microbiology

Human gut microbiome

Changes in fecal microbiota and metabolomics in a child with juvenile idiopathic arthritis (JIA) responding to two treatment periods with exclusive enteral nutrition (EEN) – Lillemor Berntson – Clinical Rheumatology

Renal Failure due to Excessive Intake of Almonds in the Absence of Oxalobacter formigenes – Yngvar Lunde Haaskjold – The American Journal of Medicine

Reanalysis of published data, no apparent new findings: Host genetics is associated with the gut microbial community membership rather than the structure – Peihua Zhao – Molecular BioSystems

Review: Modulatory Effects of Gut Microbiota on the Central Nervous System: How Gut Could Play a Role in Neuropsychiatric Health and Diseases – Shadi S Yarandi – Journal of Neurogastroenterology and Motility

Commentary: Can microbiota research change our understanding of neurodegenerative diseases? – Filip Scheperjans – Neurodegenerative Disease Management

Review: Microbes and the mind: emerging hallmarks of the gut microbiota–brain axis
– Kylynda C. Bauer – Cellular Microbiology

Animal models

Distinctly altered gut microbiota in the progression of liver disease – Guoxiang Xie – Oncotarget

Wolbachia confers sex-specific resistance and tolerance to enteric but not systemic bacterial infection in Drosophila – Radhakrishnan B Vasanthakrishnan – BioRxiv

Gut Microbiota and a Selectively Bred Taste Phenotype: A Novel Model of Microbiome-Behavior Relationships – Lyte, Mark – Psychosomatic Medicine

Periodontal dysbiosis linked to periodontitis is associated with cardio-metabolic adaptation to high-fat diet in mice – Maxime Branchereau – American Journal of Physiology Gastrointestinal and Liver Physiology

Protocol: The Gut Microbiome in the NOD Mouse – Jian Peng – Part of the series Methods in Molecular Biology

Animal microbiome

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps – Hirotaka Igarashi – Research in Veterinary Science

Plant, root, and soil microbiome

Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil – Yonatan Sher – Journal of Basic Microbiology

Selection of fungi by candidate cover crops – Maria-Soledad Benitez – Applied Soil Ecology

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils – Ellen Latz – Scientific Reports

Water and extremophile microbiome

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau – Weigang Hu – Extremophiles

Seasonal and Spatial Changes of Planktonic Bacterial Communities Inhabiting the Natural Thermal Lake Hévíz, Hungary – Gergely Krett – Acta Microbiologica et Immunologica Hungarica

Microbiome of Death

Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration –
Z.M. Burcham – Forensic Science International

Food microbiology

Review: Hygienic characteristics and microbiological hazard identification in horse and donkey raw milk – Giampaolo Colavita – Veterinaria Italiana

Waste and pollution microbiology

Microbial communities in riparian soils of a settling pond for mine drainage treatment – Miaochun Fan – Water Research

Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems – Zhitao Huang – Aquaculture International

More microbiology

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis – Sabrina Duranti – Scientific Reports

Metagenomics and bioinformatics

Not sure if this is a good approach; ignores variation between individual human microbiome strains: Reconstruction of bacterial and viral genomes from multiple metagenomes – Vineet K. Sharma – Frontiers in Microbiology

Metabolomics

Harnessing the power of microbial metabolism – Eduardo Santero – Current Opinion in Microbiology

Microbiology and art

BioArt: Joana Ricou shows the Beautiful Similarities of the Microbiome – Labiotech

Rap song: CosmosID Metagenomics: Exploring the Universe of Microbes – CosmosID – YouTube

Microbes in the news

Mythbusters: Human Microbiota – Caroline Ayinon – Yale Scientific

Introducing the “HomeGenome”. Not endorsing this. Exploring the Microcosm Within. Adventures and insights from the microbiome – Conan Milner – Epoch Times

April Fool’s Day microbiome jokes

Thanks to Microbiome Boost, Donuts May Be Beneficial: when paired with P. tursiops – Tim De Chant – PBS

A microbiology of the built environment April Fools’ joke – Jonathan Eisen – MicroBEnet

And of course my own selection: Human-derived microbial strains used for food and beverage production – Elisabeth Bik – Microbiome Digest

Science, publishing, and career

‘Lab Girl’ Is a Fierce, Uplifting, Must-Read Memoir – Hope Jahren is an acute observer, prickly, and funny as hell. – Elizabeth Royte – Elle

April 1, 2016 (the serious one)

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Make sure to check out my special April 1st post about the creative use of human-derived microbes in food and beverage production. Today’s serious update is about a twin study on oral microbiota and the effects of host genetics and smoking, microbes in floral nectar along an urbanization gradient, plankton biogeography among alpine lakes, and classification of metagenomics data.

General microbiome

Review: Compositional Data Analysis of the Microbiome: Fundamentals, Tools, and Challenges – Matthew C.B. Tsilimigras – Annals of Epidemiology

Review: Gut Microbiotas and Host Evolution: Scaling Up Symbiosis – Michael Shapira – Trends in Ecology and Evolution

Pregnancy and birth

Conference abstract: Neonatal microbiota in health and disease – P. Panigrahi – International Journal of Infectious Diseases

Human oral microbiome

Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans – Mi Young Lim – Scientific Reports

Human cervical microbiome

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Review: The effect of NOD2 on the microbiota in Crohn’s disease – Mackenzie L Lauro – Current Opinion in Biotechnology

Animal models

Prebiotics and Bioactive Milk Fractions Affect Gut Development, Microbiota and Neurotransmitter Expression in Piglets – Kirsten Berding – Journal of Pediatric Gastroenterology & Nutrition

Isolation of Lactobacillus reuteri from Peyer’s patches and their effects on sIgA production and gut microbiota diversity – Panpan Wang – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Ectomycorrhizal fungal richness declines toward the host species’ range edge – Richard A. Lankau – Molecular Ecology

Diversity and temporal dynamics of the epiphytic bacterial communities associated with the canopy-forming seaweed Cystoseira compressa (Esper) Gerloff & Nizamuddin – Francesco Paolo Mancuso – Frontiers in Microbiology

Do rhizosphere priming effects enhance plant nitrogen uptake under elevated CO2? –
Ming Nie – Agriculture, Ecosystems & Environment

Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer – Andrew B. Moyes – New Phytologist

Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient – Jacek Bartlewicz – BMC Ecology

Water and pollution microbiome

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns – Sabine Filker – Molecular Ecology

Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current – Martina A Doblin – PeerJ preprint

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water – Alexander H. Frank – Environmental Microbiology

Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay – Benjamin Misson – Science of The Total Environment

Phylogenetic clustering of fungal communities in human-disturbed streams – H. Mykrä – Ecosphere

Built environment microbiome

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system – R. P. Revetta – Journal of Applied Microbiology

Food microbiology

Biodiversity and technological-functional potential of lactic acid bacteria isolated from spontaneously fermented quinoa sourdoughs – L. Ruiz Rodríguez – Journal of Applied Microbiology

Bioreactor microbiology

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system – Daan R. Speth – Nature Communications

An exploratory study on the influence orange juice on gut microbiota using a dynamic colonic model – Ana Luiza Rocha Faria Duque – Food Research International

Bioinformatics and metagenomics

FOCUS2: agile and sensitive classification of metagenomics data using a reduced database – Genivaldo Silva – BioRxiv

Microbial Ecology

Microbial diversity arising from thermodynamic constraints – Tobias Großkopf – The ISME Journal

Techniques

Genetic circuit design automation: Programming circuitry for synthetic biology –
Alec A. K. Nielsen – Science

Review: Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display – Dragana Gagic – Frontiers in Microbiology

Microbes in the news

Your Cat’s Poop Might Help Save Lives: KittyBiome – Lisa Richman – Catster

Pine Bacteria Getting a Closer Look From Scientists – Lorena Anderson – UC Merced

Episode 2: Peek inside a lab trying to create living medicine — from bugs in your gut – Carl Zimmer – STAT News

Poop paper flushed due to possible sample contamination – Shannon Palus – Retraction Watch

About the minimal cell: Breakthrough in synthetic biology is far from ‘playing God’ – New Scientist

Commense Advances Microbiome Platform Targeting Early Childhood Health – Businesswire

New research supports previous findings in the placental microbiome – Baylor College of Medicine

Forensic microbiology from an entomological perspective – SFAM – Microbe Blog
New Potent Nanodrug to Combat Antibiotic-Resistant Infections – University of Arkansas

Vedanta Biosciences Announces License Agreement with RIKEN and other Japanese Institutions for New Immune Boosting Microbiome Technology – Pipeline Review

Brewers Claim They’ve Made Ice-Cold Beer With Vaginal Bacteria; In Theory It Works – Dana Dovey – Medical Daily

Beer brewed with vaginal bacteria is the draft we didn’t ask for – Justina Huddleston – She Knows

Scientists create ‘programming language for bacteria’ – BT.com

‘Listeria on Rye’? Many U.S. Deli Meat Slicers Cut Corners on Cleanliness – Health Day

Retail Deli Slicer Cleaning Frequency — Six Selected Sites, United States, 2012 – Laura G. Brown – CDC Morbidity and Mortality Weekly Report (MMWR)

Science, publishing, and career

Life in the lab, book review of “Lab Girl” by Hope Jahren – Meg Lowman – Science

How to Make Psychology Studies More Reliable – Ed Yong – The Atlantic

Hilda Bastian: She speaks — and draws — truth to scientific power – Karen Weintraub – STAT news

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