Category Archives: Human gut

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 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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March 31, 2016

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A special mBio issue discussing the Holobiont concept, salivary microbiota in oral cancer, truffles, sinuses in germ-free mice, and Wolbachia in cave spiders.

General microbiome

Special Issue: The Holobiont Concept- mBio
Introduction to the Hologenome Special Series – Margaret McFall-Ngai
Microbes Drive Evolution of Animals and Plants: the Hologenome Concept – Eugene Rosenberg
Speciation by Symbiosis: the Microbiome and Behavior – J. Dylan Shropshire
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts – Angela E. Douglas

Pregnancy and birth

Research Highlight: Baby steps towards the microbiome – Andrea Du Toit – Nature Reviews Microbiology

Oral microbiome

Changes in the salivary microbiota of oral leukoplakia and oral cancer – Xiaosheng Hu – Oral Oncology

Human respiratory microbiome

Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome – M. V. Tejesvi – European Journal of Clinical Microbiology & Infectious Diseases

Conference abstract: Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites – Catherine Igartua – Annals of the American Thoracic Society

Conference abstract: Gut Microbiota and Allergic Disease. New Insights
Susan V. Lynch- Annals of the American Thoracic Society

Human gut microbiome

Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes – Claudio Maffeis – Diabetes/Metabolism Research and Reviews

Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection – Braden Millan – Clinical Infectious Diseases

Special issue with reviews: Gastric and Gut Microbiota in Health and Disease – Digestive Diseases

Animal models

Effect of a long-term high-protein diet on survival, obesity development and gut microbiota in mice – Pia Kiilerich – American Journal of Physiology

Differences in the paranasal sinuses between germ-free and pathogen-free mice – Ravi Jain – International Forum of Allergy & Rhinology

Effects of taurine on gut microbiota and metabolism in mice – Haining Yu – Amino Acids

Animal microbiome

Research Highlight: Microbiome ‘coral’ations – Ursula Hofer – Nature Reviews Microbiology

Classification of Wolbachia (Alphaproteobacteria, Rickettsiales): No evidence for a distinct supergroup in cave spiders – Michael Gerth – BioRxiv

Not a great title: Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis – L. A. Ilina – Doklady Biochemistry and Biophysics

Plant, root, and soil microbiome

Screening of soil bacteria as potential agents for drugs biodegradation: a case study with clofibric acid – Claudia Popa Ungureanu – Journal of Chemical Technology and Biotechnology

Metagenomes provide valuable comparative information on soil microeukaryotes –
Samuel Jacquiod – Research in Microbiology

The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales – Gian Maria Niccolò Benucci – Microbial Ecology

Bioreactor microbiology

The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments – O. Podolich – Origins of Life and Evolution of Biospheres

Food microbiology

Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques – Hana Šuranská – Folia Microbiologica

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening – Oylum Erkus – International Journal of Food Microbiology

Bioinformatics and metagenomics

Predicting microbial interactions through computational approaches – Chenhao Li – Methods

Microbes in the news

A Hidden Factor in Stroke Severity: The Microbes in Your Gut : A new study in mice demonstrates that manipulating the microbiome can influence the extent of brain damage caused by a stroke – Jordana Cepelewic – Scientific American

Pushing and Pulling on the Mosquito Microbiome – Kevin Bonham – Scientific American

Sampling an animal shelter – Holly Ganz – MicroBEnet

Intestinal Microbiome of Children with Cystic Fibrosis Promotes Gut Inflammation, Study Finds – Patricia Inacio – Cystic Fibrosis News Today
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March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 29, 2016

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Microbiota and stroke outcome, viruses and FMT, Arctic polar deserts, sex and dorm rooms (aren’t you curious?).

Pregnancy and birth

A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker – Shelley W. Peterson – PLOS ONE

Human respiratory microbiome (see also above)

Pharyngeal carriage of Neisseria species in the African meningitis belt – Kanny Diallo – Journal of Infection

Human gut microbiome

Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells – Corinne Benakis – Nature Medicine

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation – Christel Chehoud – mBio

Correlation between diet and gut bacteria in a population of young adults – Lino Mayorga Reyes – International Journal of Food Sciences and Nutrition

Fecal Microbiota Transfer in Patients With Chronic Antibiotic-Refractory Pouchitis – Andreas Stallmach – American Journal of Gastroenterology

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Review: Metabolic role of lactobacilli in weight modification in humans and animals – Fatima Drissi – Microbial Pathogenesis

Editorial: The Dawning of Microbiome Remediation for Addressing Antibiotic Resistance – Alison Laufer Halpin – Clinical Infectious Diseases

Review: Beyond Antibiotics: New Therapeutic Approaches For Bacterial Infections – Alan R. Hauser – Clinical Infectious Diseases

Correspondence: The Microbiome: A Biological Mechanism Underpinning the Social Gradient of Musculoskeletal Conditions? – Sharon L Brennan-Olsen – Journal of Bone and Mineral Research

Animal models

Effects of chlorpyrifos on the gut microbiome and urine metabolome in mouse (Mus musculus) – Yanping Zhao – Chemosphere

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites – Jan Kopecky – PLOS ONE

Animal microbiome

Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species – Ming-Ming Su – PLOS ONE

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions – Philipp Hennersdorf – PLOS ONE

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

Plant, root, and snow microbiome

Diversity and distribution of the endophytic bacterial community at different stages of Eucalyptus growth – Paulo Sérgio Balbino Miguel – Antonie van Leeuwenhoek

Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book: Microbial-mediated Induced Systemic Resistance in Plants
Editors: Devendra K. Choudhary, Ajit Varma – Springer

Water, snow, and extremophile microbiome

Microbial communities in a High Arctic polar desert landscape – Clare M. McCann – Frontiers in Microbiology

Responses of methanogenic and methanotrophic communities to warming in varying moisture regimes of two boreal fens – Krista Peltoniemi – Soil Biology and Biochemistry

Oligotyping and metagenome analyses reveal a high-resolution recurrence that frames potential ecological strategies of North Sea bacterioplankton – M. Chafee – Annual DOE JGI Genomics of Energy & Environment Meeting

Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities – Luis N. Morgado – Global Change Biology

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico – Marshall Bowles – Deep Sea Research Part II: Topical Studies in Oceanography

Surface waters in northern Tanzania harbor fecal coliform and antibiotic resistant Salmonella spp. capable of horizontal gene transfer – Beatus Lyimo – African Journal of Microbiology Research

Book chapter: Planktonic Bacterial Communities in Mountain Lake Ecosystems – Masanori Fujii – Structure and Function of Mountain Ecosystems in Japan

Waste and pollution microbiome

Biodegradation of dispersed Macondo crude oil by indigenous Gulf of Mexico microbial communities – Jian Wang – Science of The Total Environment

The effects of various land reclamation scenarios on the succession of soil Bacteria, Archaea, and fungi over the short and long term – Junjian Li – Frontiers in Ecology and Evolution

Illumina MiSeq sequencing reveals long-term impacts of single-walled carbon nanotubes on microbial communities of wastewater treatment systems – Yuanyuan Qu – Bioresource Technology

Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters – Jing Gao – Bioprocess and Biosystems Engineering

Built environment microbiome

Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants – Julia C Luongo – Indoor Air

Microbiological characterization of stable resuspended dust – Nora Kováts – Int J Occup Med Environ Health

Food microbiome

Reducing bias in complex microbial community analysis in shrimp based on propidium monoazide combined with PCR-DGGE – Fei Zhao – Food control

A simple and rapid method for detecting living microorganisms in food using laser speckle decorrelation – Jonghee Yoon – arXiv

Viruses and phages

A strange endocytobiont revealed as largest virus – P Scheid – Current Opinion in Microbiology

More microbiology

A generalized spatial measure for resilience of microbial systems – Ryan S. Renslow – Frontiers in Microbiology

Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes – Felipe L. Pereira – Genomics

In Vitro Selection of RNA-cleaving DNAzymes for Bacterial Detection – Wenqing Zhang – Methods

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution – Knut Drescher – PNAS

Book: New Weapons to Control Bacterial Growth – Editors: Tomas G. Villa, Miguel Vinas – Springer

Microbes in the news

How bacteria, fungi, and mold are finding a home in high-end kitchens
Scientists and chefs find flavor through fermentation – Lindsey J. Smith – The Verge

Could bugs in the gut offer clues for reducing the severity of stroke? – Eric Boodman – STAT news

Microbial cocktails join fecal transplants in IBD treatment trials –
Mark Ratner – Nature Biotechnology News

The Fridge Laser That Detects Bacteria Crawling All Over Food – Rachel Metz – Technology Review

What bacteria lurk in stable dust? – Horsetalk

Humans use ‘sticky molecules’ to hang on to good bacteria in the gut – Stuart Gillespie – University of Oxford

Clostridium botulinum: New Details Emerge on a Notorious Bird-Killing Bacteria – Matt Soniak – Audubon

Swiss study finds E. coli bacteria in ice cubes – The Local

How Dirty Are Public Restrooms, Really? – Stephanie Pappas – Live Science

Gut Microbes Can Evolve From Foe to Friend—And Do It Fast – Ed Yong – National Geographic

Oyster research could lead to food safety strategies – Cookson Beecher – Food Safety News

Why a healthy gut may be the secret to a lean, healthy body – Jennifer Landa – Fox News

Does the 5-Second Rule When You Drop Food Really Work? Here’s What Science Says – Jessica Eggert – Science.Mic

Science, publishing, and career

The seagull of science: Google’s bold bid to transform medicine hits turbulence under a divisive CEO – Charles Piller – STAT news

Andrew Kern on PLoS: Things aren’t what they seem – Storify

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March 28, 2016

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Oral microbiome and smoking, a bacterial genome from a germ-free mouse isolate, semi-arid soils, jellyfish, OTU picking methods, and the best hypervariable regions in the 16S rRNA gene.

Human oral microbiome

Cigarette smoking and the oral microbiome in a large study of American adults – Jing Wu – The ISME Journal

Human gut microbiome

Persisting changes of intestinal microbiota after bowel lavage and colonoscopy – Drago, Lorenzo – European Journal of Gastroenterology & Hepatology

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations – Rashmi Sinha – PLOS ONE

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India – Saurabh Kedia – Journal of Gastroenterology

Review: Gut Microbiota and Lifestyle Interventions in NAFLD – David Houghton – MDPI International Journal of Molecular Sciences

Review: Microbiota-gut-brain signalling in Parkinson’s disease: Implications for non-motor symptoms – Valeria D. Felice – Parkinsonism & Related Disorders

PhD Thesis: Development and analysis of molecular methods for functional metagenomics of the human gut microbiome – Kathy Lam – University of Waterloo

Animal models

Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease – Irina A. Kirpich – The American Journal of Pathology

Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse – T. A. Auchtung – Genome Announcements

Animal microbiome

Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes – Daniel F. R. Cleary – FEMS Microbial Ecology

Review: Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases – Mikolaj M. Raszek – Frontiers in Genetics

Plant, root, and soil microbiome

Soil characteristics driving arbuscular mycorrhizal fungi communities in semiarid Mediterranean soils – Maria del Mar Alguacil – Applied and Environmental Microbiology

454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems – Elham A. Kazeeroni – Frontiers in Plant Science

Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis – Zhiyuan Yao – Journal of Soils and Sediments

Soil communities are affected by CO2 belowground emissions at a natural vent in Spain – I. Fernández-Montiel – Soil Biology and Biochemistry

No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium) – Florine Degrune – Agriculture, Ecosystems & Environment

Bacteria play a more important role than nutrients in the accumulation of tetracycline resistance in manure-treated soil – Shuang Peng – Biology and Fertility of Soils

Review: Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism – Sofie Thijs – Frontiers in Microbiology

Water microbiome

Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids – Jean-Paul Baquiran – Frontiers in Microbiology

Streams: Regional and global elevational patterns of microbial species richness and evenness – Jianjun Wang – Ecography

Extremophile microbiome

Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes – Daniel R. Colman – Frontiers in Microbiology

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments – Alexander Crits-Christoph – Frontiers in Microbiology

Bioinformatics and metagenomics

Application of database-independent approach to assess the quality of OTU picking methods – Patrick D Schloss – BioRxiv

MG-Digger: an automated pipeline to search for giant virus-related sequences in metagenomes – Jonathan Verneau – Frontiers in Microbiology

MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices – Dinghua Li – Methods

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis – Bo Yang – BMC Bioinformatics

Absent words and the (dis)similarity analysis of DNA sequences: an experimental study – Mohammad Saifur Rahman – BMC Research Notes

Book chapter: Bidirectional Variable-Order de Bruijn Graphs – Djamal Belazzougui – LATIN 2016: Theoretical Informatics

Transcriptomics

Review: Translating RNA sequencing into clinical diagnostics: opportunities and challenges – Sara A. Byron – Nature Reviews Genetics

Techniques

Modification of a high- throughput automatic microbial cell enumeration system for ship board analyses – Christin M. Bennke – Applied and Environmental Microbiology

More microbiology

Rare-earth elements: Rare-earth separation using bacteria – William Bonificio – Environmental Science & Technology Letters

Expression of HIV-1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus – Angela Marcobal – AIDS Research and Human Retroviruses

Review: Studying Bacterial Multispecies Biofilms: Where to Start? – Henriette L. Røder – Trends in Microbiology

Microbes in the news

Osel scientists engineer vaginal lactobacillus to express neutralizing HIV-1 antibody fragments – EurekAlert

‘Good’ bacteria could save amphibians hit by fungal diseases – Adam Wernick – PRI

Forget Chocolate Rabbits: Microbiologists Celebrate Easter With Bacteria Bunny – ABC News

Psychobiotics Will Use Bacteria to Alter Your Brain Through Your Gut – Ben Guarino – Inverse

Low FODMAP diet may significantly improve IBS symptoms – Healio

Scientists to drill into dinosaur-killing blast – Eric Hand – Science

Rage Disorder Linked with Parasite Found in Cat Feces. Toxoplasmosis may alter brain chemistry is people exhibiting bouts of explosive anger – Christopher Wanjek – Scientific American

Bacteria Hysteria

Would you dare to bacteria-test your entire life? Katherine Keogh did … and the result will shock all house-proud readers – Katherine Keogh – Daily Mail

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March 24, 2016

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Two papers on antibiotics in early childhood and obesity, diabetic foot ulcers, vertebrate animal microbiomes, cattle hides, kimchi, human archaeological remains, and high inter-center variability in microbiome results.

General microbiome

Review: Stress as a Normal Cue in the Symbiotic Environment – Julia A. Schwartzman – Trends in Microbiology

Pregnancy and birth

Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity – Frank I. Scott – Gastroenterology

Antibiotic Exposure During the First 6 Months of Life and Weight Gain During Childhood – Jeffrey S. Gerber – JAMA

Editorial: From Bottles to Diapers: How Manipulating and Exploring the Microbiome Is Defining Newborn Care – Jill L. Maron – Clinical Therapeutics

Research highlight: Gut microbiota dysbiosis precedes NEC – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Human skin microbiome

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers – Karen Smith – BMC Microbiology

Human gut microbiome

Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents – R. Alan Harris – Journal of Immunology Research

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling – Nicholas Edward Ilott – The ISME Journal

Targeting colorectal cancer-associated bacteria: a new area of research for personalized treatments – T. Faïs – Gut Microbes

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study – Borgo Francesca – Childhood Obesity

Review: Can attention to the intestinal microbiota improve understanding and treatment of anorexia nervosa? – Jacquelyn Carr – Expert Review of Gastroenterology & Hepatology

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: FoMenTing Change? – Flaviano S. Martins – Digestive Diseases and Sciences

Review: Does the Microbiome Cause B27-related Acute Anterior Uveitis? – James T. Rosenbaum – Ocular Immunology and Inflammation

Microbes in blood

The prognostic significance of bacterial DNA in patients with decompensated cirrhosis and suspected infection – Tony Bruns – Liver International

Animal models

The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy – Gut Microbes

TLR4-Dependent Secretion by Hepatic Stellate Cells of the Neutrophil-Chemoattractant CXCL1 Mediates Liver Response to Gut Microbiota – Amélie E. Bigorgne – PLOS ONE

Animal microbiome

Vertebrate bacterial gut diversity: size also matters – Jean-Jacques Godon – BMC Ecology

Larval growth rate is associated with the composition of the gut microbiota in the Glanville fritillary butterfly – L. Ruokolainen – Oecologia

Host origin and tissue-microhabitat shaping the microbiota of the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – FEMS Microbiology Ecology

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides – Jessica Chopyk – Microbiome

Plant, root, and soil microbiome

High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – The Journal of Eukaryotic Microbiology

Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe – Jing Zhang – Scientific Reports

Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains – Manila Yadav – BMC Microbiology

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols – Huili Yu – Microbiology Open

Bioprospecting plant-associated microbiomes – Christina A. Müller – Journal of Biotechnology

Water and extremophile microbiome

Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters – Christoph Reitschuler – Antonie van Leeuwenhoek

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics – Alexandra Meziti – Environmental Microbiology

Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting – Dimitri Meier – Environmental Microbiology

Waste and pollution microbiology

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates – Vrutika Patel – BMC Microbiology

Built environment microbiology

Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system – Jenni Inkinen – Journal of Applied Microbiology

Forensic microbiology

Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains – Romy Müller – Journal of Archaeological Science

Food microbiology

Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable – Young Joon Oh – Antonie van Leeuwenhoek

Computational modeling

Host Selection of Microbiota via Differential Adhesion – Kirstie McLoughlin – Cell Host & Microbe

Techniques

The real cost of sequencing: scaling computation to keep pace with data generation – Paul Muir – Genome Biology

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability – Andreas Hiergeist –
International Journal of Medical Microbiology

Genotyping bacterial and fungal pathogens using sequence variation in the gene for the CCA-adding enzyme – Paul Franz – BMC Microbiology

Proteomics

Review: Tackling probiotic and gut microbiota functionality through proteomics – Lorena Ruiz – Journal of Proteomics

Microbes in the news

Can we model how viruses move between species? – Nancy Mendoza – Microbe Post

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More – Jon Palfreman – PBS

Report: Laminate wood flooring risk was underestimated by CDC – Jonathan Eisen – MicroBEnet

Microbiota profiles in patients with colorectal cancer differ from healthy individuals – Healio

Science, publishing and career

Set up a ‘self-retraction’ system for honest errors, says Daniele Fanelli – Nature

Incorporating Primary Scientific Literature in Middle and High School Education – Sarah C. Fankhauser – ASM Science

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