Category Archives: Infection and transplantation

November 4, 2015

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Lots of upcoming workshops and seminars, genome-wide association of the human gut microbiota, contamination of cord blood units, and bacteria with the rRNA genes on a plasmid, not on their chromosome.

Events

Webinar: The ageing microbiota by Gemma Walton and Annie-Rose Harrison-Dunn – November 17, 2015 – 10AM Paris

Mothur 3-day workshop organized by Pat Schloss – December 16-18, Detroit.

2nd Microbiome R&D and Business Collaboration Congress: Asia – February 29-March 1 2016, Kuala Lumpur, Malaysia

Early career workshop on Microbiology of the built environment (Chicago, IL) – Jack Gilbert lab – April 26-29 2016

Human oral microbiome

Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes – Meng Zhang – PLOS ONE

Human gut microbiome

In Hutterites: Genome-Wide Association Studies of the Human Gut Microbiota – Emily R. Davenport – PLOS ONE

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

Infection microbiology

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling – Luís França – PLOS ONE

More microbes

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome – Mizue Anda – PNAS

High-throughput 3D tracking of bacteria on a standard phase contrast microscope –
K.M. Taute – Nature Communications

Automated image analysis for quantification of filamentous bacteria – Marlene Fredborg – BMC Microbiology

Microbial ecology

Community rescue in experimental metacommunities – Etienne Low-Décarie – PNAS

Microbes in the news

Family dog lowers kids’ asthma risk, proving dirt and bacteria are good for children – Shelley Hazen – Inquisitr

Microbiome expert Martin Blaser to receive Georgetown’s Cura Personalis Award Nov. 3 – EurekAlert

Microbiomes could prove essential in various fields of science, study suggests – Kimberly Nielsen – The Daily Californian

Salivary microbiome of whitetail deer: Mature doe set the rut timetable – Oak Duke – Wellsville Daily Reporter

Finally! New germ exhibit opening at the American Museum of Natural History – Rebecca Rosenthal – North Jersey

Thank heavens, someone figured out which bacteria live on a donkey’s penis – Discover
http://blogs.discovermagazine.com/seriouslyscience/2015/11/03/thank-heavens-

How was the bacteria at York Hospital found?– Dylan Segelbaum – York Daily Record

Worms (and germs) may be the answer to preventing allergies – Jason Tetro – Popular Science

Two Million-Year-Old Bacteria Used Iron “Sunscreen” – Charlotte Ward – RedBrick

Bacteria infecting orange groves is driving up cost of juice; threatens nation’s supply – Sandy Miller – Fox2Now

Science, publishing, and career

EU urges science publishers to adapt to open access: European research commissioner Carlos Moedas has urged journal publishing companies to reshape their business models to an open access system. – LabNews

Supervision: Clear direction: Managing laboratory members as well as a research strategy can be difficult for early-career principal investigators, but help is at hand. – Boer Deng – Nature

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November 2, 2015

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Overview of key players of the human microbiome in different sites, foals are born with a rich gut microbiome, biogeography of salmon microbiome, bacteria on Chinese glaciers, and the effect of X-rays on the mango microbiome.

General human microbiome

Diversity of key players in the microbial ecosystems of the human body – Ferenc Jordán – Scientific Reports

Pregnancy and birth

Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing – Hiroshi Murakami – Pediatric Surgery International

Review: Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics – Mohsin Khurshid – Future Microbiology

Review: Introduction : Microbiome in human reproduction – Jason M. Franasiak – Fertility and Sterility

Correspondence: Vaginal microbiota during pregnancy: Pathways of risk of preterm delivery in the absence of intrauterine infection? – Jeffrey A Keelan – PNAS

Reply to Keelan and Payne: Microbiota-related pathways for preterm birth – Daniel B DiGiulio – PNAS

Human oral microbiome

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation – Brenda P.F.A. Gomes – Journal of Endodontics

Oral microbiota in patients with atherosclerosis – Frida Fåk – Atherosclerosis

Review: Intermicrobial interactions as a driver for community composition and stratification of oral biofilms – Nicholas S. Jakubovics – Journal of Molecular Biology

Review: The Fungal Biome of the Oral Cavity – Jyotsna Chandra – Candida Species

Human respiratory microbiome

Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes – Alexandra Zimmermann – Journal of Medical Microbiology

Human gut microbiome

Donor species richness determines fecal microbiota transplantation success in inflammatory bowel disease – Severine Vermeire – Journal of Crohn’s and Colitis

Gut mucosal microbiome across stages of colorectal carcinogenesis – Geicho Nakatsu – Nature Communications

Review: Gut mycobiota and adenomas – Chunguang Luan – Gut Microbes

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Animal microbiome

Development of the faecal microbiota in foals – M. C. Costa – Equine Veterinary Journal

Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment – Saria Otani – Microbial Ecology

The biogeography of the atlantic salmon (Salmo salar) gut microbiome – Martin S Llewellyn – The ISME Journal

Exposure to West Nile Virus Increases Bacterial Diversity and Immune Gene Expression in Culex pipiens – Steven D. Zink – Viruses

Plant, root, and soil microbiome

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture – Linkun Wu – Scientific Reports

Drivers of bacterial beta diversity in two temperate forests –  Wang – Ecological Research

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing – Chris Munday – Aerobiologia

Review: Influence of soil microbiota in nurse plant systems – Susana Rodríguez-Echeverría – Functional Ecology

Review: The Role of Plant–Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants – Nele Weyens – International Journal of Molecular Sciences

Water and extremophile microbiome

Metagenomic analysis of the bacterial community of the Sea of Azov – D. G. Matishov – Marine Biology

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India – Jhasketan Badhai – Frontiers in Microbiology

High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing – Qing Liu – Systematic and Applied Microbiology

Review: Databases of the marine metagenomics – Katsuhiko Mineta – Gene

Waste microbiology

Changes in Microbial Composition of Wastewater During Treatment in a Full-Scale Plant – Marija Kaevska – Current Microbiology

Wastewater treatment and microbial communities in an integrated photo-bioelectrochemical system affected by different wastewater algal inocula – Li Xiao – Algal Research

Review: Microbial diversity in support of anaerobic biomass valorization – M. Jobard – Critical Reviews in Biotechnology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – Barakat S M Mahmoud – Letters in Applied Microbiology

Metagenomics and bioinformatics

Poster: Alignment-free methods for metagenomic profiling – Shanshan Gao – BMC Bioinformatics

Infection microbiology

Microbial diversity on intravascular catheters from paediatric patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Phages and viruses

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile – Pierre Boudry – mBio

Microbial Ecology

Do modern theories of biodiversity fail to predict commonness and rarity among microbes? – William R. Shoemaker – PeerJ

Strongly Deterministic Population Dynamics in Closed Microbial Communities – Zak Frentz – Physical Review

Microbes in the news

Scientists debate mega-microbiome initiatives: Research standards will advance the field, proponents say, but critics counter that they will stifle creativity – Rachel Becker – Nature

Foals born with rich microbial community in their gut – study – Horsetalk

Halloween: Monster Microbiology, 101: If werewolves and other ghouls existed, they’d surely have microbiomes – Rob Dunn – Science Friday

Bacteria in space – ‘You cannot just open the window’ – Interview with Ralf Möller about microbes found on the ISS – DW

New technique could prevent biofilms on catheters and medical implants – EurekAlert

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October 29, 2015

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Library prep technology, skin communities in urban and rural populations, rarity in aquatic microbes, and the microbiome of solar panels.

Pregnancy and birth

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons – Anuradha Ravi – Scientific Reports

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life – Tanya L Alderete – The American Journal of Clinical Nutrition

Human skin microbiome

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations – Shi Ying – PLOS ONE

Human respiratory microbiome

Review: A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS) – Mahboobeh Mahdavinia – Clinical & Experimental Allergy

Human gut microbiome

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

DGGE: The duodenal microbiota composition in children with active coeliac disease is influenced for the degree of enteropathy – F. Girón Fernández-Crehuet – Anales de Pediatría (English Edition)

Review: The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases – Ana Luisa Neves – Current Opinion in Pharmacology

Review: Microbiome impact on metabolism and function of sex, thyroid,
growth and parathyroid hormones – Michał Kunc – Acta Biochimica Polonica

Review: Intestinal Microbiota: From Inflammatory Bowel Disease to Bone Marrow Transplantation – Ernst Holler – Blood

Review: Dysbiotic gut microbiome: A key element of Crohn’s disease – Styrk Furnes Øyri – Comparative Immunology, Microbiology and Infectious Diseases

Infection microbiology

Serum bacterial DNA detection in patients with cholangitis after Kasai procedure – Qianfu Luo – Pediatrics International

Deceiving title (not about microbiome but infection): Breast Implant–Associated Infections: The Role of the National Surgical Quality Improvement Program and the Local Microbiome – Cohen, Justin B. – Plastic and Reconstructive Surgery

Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration – Dagmar Chudobova – The Brazilian Journal of Infectious Diseases

Animal and bioreactor models

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia – Tim J Schuijt – Gut

In mice: The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation – Mario M. Zaiss – Cell

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization – Malin E.V. Johansson – Cell Host & Microbe

Microbiota-Dependent Hepatic Lipogenesis Mediated by Stearoyl CoA Desaturase 1 (SCD1) Promotes Metabolic Syndrome in TLR5-Deficient Mice – Vishal Singh – Cell Metabolism

Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing – Yongchao Xie – Chemosphere

The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals – A. Schoster – Equine Veterinary Journal

A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs – Corrin Wallis – Veterinary Microbiology

Assessment of prebiotic potential of Akpan-yoghurt-like product and effects on the human intestinal microbiota – Beatriz Gullón – Journal of Functional Foods

Relationship between inflammation, the gut microbiota, and metabolic osteoarthritis development: studies in a rat model – K.H. Collins – Osteoarthritis and Cartilage

Plant, root, and soil microbiome

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem – Claudia M. Boot – Soil Biology and Biochemistry

Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil? – Erik Verbruggen – Journal of Ecology

Editorial: Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Water microbiome

Review: Rarity in aquatic microbes: placing protists on the map – Ramiro Logares – Research in Microbiology

Waste microbiology

Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion – Eoin Gunnigle – FEMS Microbiology Ecology

An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge – D.J. Beale – Water Research

Extremophile microbiome

Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community – Alexander Crits-Christoph – BioRxiv

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city – Pedro Dorado-Morales – BioRxiv

Food microbiology

Microbial community dynamics in thermophilic undefined milk starter cultures – Eugenio Parente – International Journal of Food Microbiology

Metagenomics and bioinformatics

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition – David Koslicki – PLOS ONE

Linear-time superbubble identification algorithm for genome assembly – Ljiljana Brankovic – Theoretical Computer Science

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut – Christian Milani – Scientific Reports

Power law analysis of the human microbiome – Zhanshan (Sam) Ma – Molecular Ecology

More microbiology

Bioactive natural products from novel microbial sources – Victoria L. Challinor – Annals of the New York Academy of Sciences

Conference report: Bacterial Networks in Cells and Communities – Victor Sourjik – Journal of Molecular Biology

Self-establishing communities enable cooperative metabolite exchange in a eukaryote – Kate Campbell – eLife

Techniques

Library preparation methodology can influence genomic and functional predictions in human microbiome research – Marcus B. Jones – PNAS

Microbes in the news

Scientists Urge National Initiative on Microbiomes – Carl Zimmer – New York Times

Fecal transplant pills: Large-scale production begins: Nonprofit stool bank launched by MIT researchers completes first dose-finding study – GlobeNewsWire
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October 22, 2015

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Digesting from LAX: Risk of childhood asthma, antibiotic effects on fish microbiome, and interactions between the gut microbiome and Clostridium difficile.

Pregnancy and birth

Claims that placenta has a rich microbiome, which I disagree with. The maternal microbiome and pregnancy outcomes – Chelsea Fox – Fertility and Sterility

Human gut microbiome

Altered fecal short chain fatty acid composition in children with a history of Hirschsprung-associated enterocolitis – Farokh R. Demehri – Journal of Pediatric Surgery

Gut microbiota and the risk of childhood asthma – Priya Venkatesan – The Lancet Respiratory Medicine

Can Helminth Infection Reverse Microbial Dysbiosis? – P’ng Loke – Trends in Parasitology

Can a Bug in the Gut Act Like a Drug in the Brain? – Robert H. Howland – Journal of Psychosocial Nursing

Review: Interactions Between the Gastrointestinal Microbiome and Clostridium difficile – Casey M. Theriot – Annual Review of Microbiology

Animal models

Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure – Sarah M. Bahr – EBioMedicine

Fish: The host effects of Gambusia affinis with an antibiotic-disrupted microbiome – Jeanette M. Carlson – Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Host and microbiota interactions are critical for development of murine Crohn’s-like ileitis – M Roulis – Mucosal Immunology

Plant, root, and soil biology

Drought-induced piñon mortality alters the seasonal dynamics of microbial activity in piñon–juniper woodland – Daniel D. Warnock – Soil Biology and Biochemistry

Long-term oil contamination increases deterministic assembly processes in soil microbes – Yuting Liang – Ecological Applications

Water microbiome

A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor Igneous Crust – Magnus Ivarsson – PLOS ONE

Food microbiology

Review: Microbial terroir and food innovation: the case of yeast biodiversity in wine – Vittorio Capozzi – Microbiological Research

Review: Microbiome profiling in fresh-cut products – Chiara Gorni – Trends in Food Science & Technology

Infection

Why Do We Feel Sick When Infected—Can Altruism Play a Role? – Keren Shakhar, Guy Shakhar – PLOS Biology

Microbes in the news

Gut researcher issues warning on DIY poo transplants: Q&A with Dr Paul Bertrand on the pros and cons of poo transplants to treat bacterial infections – Jess Davis
– SBS

Surprising source for ancient life biomarker found: It was thought that tetrahymanol was produced primarily by eukaryotes, but a new study suggests many bacteria might also produce the lipid – Stanford

Science, publishing, and career

Why biomedical superstars are signing on with Google. Tech firm’s ambitious goals and abundant resources attract life scientists – Erika Check Hayden – Nature

The Rise of “Quit Lit”: Soon-to-be former academics are taking their grievances public – Colleen Flaherty – Slate
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October 19, 2015

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None of the Elsevier links from my PubMed alert worked today, and I could not find the articles through other searches. So just a short digest with polymicrobial DNA in sepsis patients and a collection of pre-antibiotic bacteria.

Infection microbiome

The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients – MMP Faria – BMC Microbiology

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis – Alexander L. Greninger – Genome Medicine

Microbiome models

The gut microbiota modulates host amino acid and glutathione metabolism in mice – Adil Mardinoglu – Molecular Systems Biology

Microbiome engineering could select for more virulent pathogens – Luke McNally – BioRxiv

Plant, root, and soil microbiome

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments – Özge Eyice – Archives of Microbiology

Other microbiology

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource – Kate S. Baker – Genome Medicine

Microbes in the news

Mac researcher eyes gut bacteria in preventing celiac disease: Elena Verdú – Joanna Frketich – Hamilton Spectator

This is of concern: No time to take safety training, says infected microbiology lab supervisor: report – Ruth Bonneville – Winnipeg Free Press

A super short microbial tour of Paris tombs – Rosin Cerate

How a 500-year experiment to revive dormant microbes could reveal the secrets to cheating time – Alex Riley – Aeon
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October 4, 2015

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Pregnancy and birth

Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children – Jing Cheng – ISME Journal

Transplantation and infection microbiology

How’s your microbiota? Let’s check your urine. – Robert R. Jenq – Blood
Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome – Daniela Weber – Blood

Next-Generation Sequencing for Infectious Disease Diagnosis and Management : A Report of the Association for Molecular Pathology – Martina I. Lefterova – The Journal of Molecular Diagnostics

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Human gut microbiome

The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology – Kleiman, Susan C. – Psychosomatic Medicine

Interview: The Relationship Between the Gut Microbiota and Liver Disease – Jasmohan S. Bajaj – Gastroenterology & Hepatology

Animal models

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides – Meng Wu – Science

Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms: Part 2. Role of Gut Microorganisms – Yu Yang – Environmental Science & Technology

Animal microbiome

An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus – Joseph A. Hakim – Frontiers in Microbiology

Plant, root, and soil microbiome

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance – Hiromi Kato – DNA Research

Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica – Ying-wu Shi – Journal of Microbiology

Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan – Yu Fukasawa – Fungal Ecology

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities – Ye Deng – Global Change Biology

Waste microbiology

Contrasting microbial community composition and function perspective in sections of a full-scale coking wastewater treatment system – Shuang Zhu – Environmental Biotechnology

Microbial interactions and implications for oil biodegradation process in mangrove sediments – Adriana Daudt Grativol – PeerJ Preprint

Extremophiles

Subsurface Halophiles: An Analogue for Potential Life on Mars – Woolman, P. F – The Open University

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond – Addis Simachew – Microbiology of Aquatic Systems

Conference Abstract: Life on the frozen continent: diversity of RuBisCO, nifH and pufLM genes in soils around the Princess Elisabeth Station, Sør Rondane Mountains, Antarctica – Guillaume Tahon – Ghent University

Bioinformatics, mathematical models, metagenomics

Habitat Fluctuations Drive Species Covariation in the Human Microbiota – Charles K. Fisher – BioRxiv

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Metabolomics, Proteomics

Video: An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis – David Colatriano, David A. Walsh – JoVE

Rumen microbial communities influence metabolic phenotypes in lambs – Diego P. Morgavi – Frontiers in Microbiology

Phages and viruses

The Tailocin Tale: Peeling off Phage Tails – Maarten G.K. Ghequire and René De Mot- Trends in Microbiology

Functional foods

Review: Prebiotics: why definitions matter – Robert W Hutkins – Current Opinion in Biotechnology

Microbes in the news

Microbiome Meals: Researchers identify a handful of genes that help bacteria in the mouse gut adapt to dietary changes – By Rina Shaikh-Lesko – The Scientist

Signature dishes: As people pass through life they leave a trail of bacteria in their wake – Economist

Chronic kidney disease and its effect on microbiome metabolism – American Microbiome Institute

Recap: Gut microbiome conference September 2015, Huntington Beach – UNC Center of Excellence for Eating Disorders

Nominations sought for NAS Committee on Microbiomes of the Built Environment – Jonathan Eisen – MicroBEnet

Legionnaires’ Bacteria Regrew in Bronx Cooling Towers That Were Disinfected – Benjamin Mueller – New York Times

NYU professor to chair presidential council on antibiotic bacteria resistance – Farhin Lilywala – Washington Square News

You say microbiota, I say microbiome: The 8 word guide to the microbiota – James Vitale – Taconic

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October 1, 2015

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October already! Today I’ve got two microbiome symposia for you, microbiome imaging, early antibiotics and asthma risk, and virome sequencing.

Events

Second Annual Microbiome Symposium – October 28-29 – CHMI / Penn Vet Center for Host Microbial Interactions – Philadelphia, USA (click on tab “Symposium 2015 at the bottom part), featuring talks by Handelsman, Relman, Grice, Dominguez-Bello, Mills, and Gewirtz.

Second Microbiome R&D and Business Collaboration Congress: Asia – Feb 29-March 1, 2016 – Kuala Lumpur, Malaysia.

General microbiome

Review: Microbial Malaise: How Can We Classify the Microbiome? – Robert G. Beiko – Trends in Microbiology

Review: Early Life Adversity and Brain Development: Is the Microbiome a Missing Piece of the Puzzle? – S.M. O’ Mahony – Neuroscience

Review: American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome – Clay F. Semenkovich – Diabetes

Pregnancy and birth

Editorial: Asthma: Undoing millions of years of coevolution in early life? – Maria Gloria Dominguez-Bello and Martin J. Blaser – Science Translational Medicine
Belongs to: Early infancy microbial and metabolic alterations affect risk of childhood asthma – Marie-Claire Arrieta – Science Translational Medicine

Human skin microbiome

Review: The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights – Elizabeth A. Grice – Genome Research

Human gut microbiome

Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy – Tasha M. Santiago-Rodriguez – PLOS ONE

Review: The gut microbiome in NAFLD and ALD – Irina A. Kirpich – Clinical Liver Disease

Review: Prebiotic and Probiotic Regulation of Bone Health: Role of the Intestine and its Microbiome – Laura McCabe – Current Osteoporosis Reports

Animal models and bioreactors

Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome – Da-Hai Yu – Genome Biology

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs) – Jennifer M. Auchtung – Microbiome

Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Quantitative Imaging of Gut Microbiota Spatial Organization – Kristen A. Earle – Cell Host & Microbe

Increased Bacterial Load and Expression of Antimicrobial Peptides in Skin of Barrier-Deficient Mice with Reduced Cancer Susceptibility – Ken Natsuga – Journal of Investigative Dermatology

Animal Microbiome

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem – Susana Rodríguez-Marconi – PLOS ONE

Surveys for maternally-inherited endosymbionts reveal novel and variable infections within solitary bee species – Abiya Saeed – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Assessing the ecological status of seagrasses using morphology, biochemical descriptors and microbial community analyses. A study in Halophila stipulacea (Forsk.) Aschers meadows in the northern Red Sea – Astrid Y. Mejia – Ecological Indicators

The effects of exotic weed Flaveria bidentis with different invasion stages on soil bacterial community structures – Chaohe Huangfu – African Journal of Biotechnology

Water microbiome

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific – Mark T. Price – Frontiers in Microbiology

Spatial–temporal variations and diversity of the bacterioplankton communities in the coastal waters of Kuwait – Awatef Almutairi – Marine Pollution Bulletin

Review: Substratum-Associated Microbiota: benthic algae and bacteria from a range of aquatic environments – Paula C. Furey – Water Environment Research

Waste and composting microbiology

Limited dissemination of the wastewater treatment plant core resistome – Christian Munck – Nature Communications

Neglected role of fungal community composition in explaining variation in wood decay rates – A. van der Wal – Ecology

Metagenomics

Enhanced virome sequencing through solution-based capture enrichment –
Todd N Wylie – Genome Research

Metabolic networks

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity – Tasia M. Taxis – Nucleic Acids Research

Microbes in the news

Missing Microbes Provide Clues About Asthma Risk – Rob Stein – NPR (see above)
Study Links Asthma to Low Levels of Gut Bacteria in Newborns – Gautam Naik – Wall Street Journal

New test detects all viruses that infect people, animals – EurekAlert (see above)

Your gut development during infancy can have lifelong implications – Baylor College of Medicine – EurekAlert

Biologists Say Breeding Better Soil Microbes Can Help Grow Bigger Plants – Kiona Smith-Strickland – Gizmodo

Diets Rich in Vegetables May Reduce Heart Disease Risk Through Microbiome Changes – Medical Research

TU Delft students win on world stage with 3D bacteria printer – Materia

The headlines are getting weirder and weirder, but here we go: Ancient bacteria could be ‘elixir of life’ after it makes elderly mice ‘begin to dance’ and produce offspring – Andrew Griffin – Independent

Better Gut Microbiota Shift With Bypass vs Sleeve Gastrectomy – Becky McCall – Medscape

Sounds like trying to find a radio station on the wrong band: Scientists synthesise sound of single bacterium swimming – Bernie Hobbs – ABC Australia

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September 24, 2015

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Human genetic variation and microbiome composition, turmeric & travel, Nicotiana recruitment, and microbial stress in the city.

General microbiome

Editorial: Host genetic architecture and the landscape of microbiome composition: humans weigh in – Andrew K Benson – Genome Biology

Host genetic variation impacts microbiome composition across human body sites
Ran Blekhman – Genome Biology

Database of host-pathogen and related species interactions, and their global distribution – Maya Wardeh – Scientific Data

Pregnancy and birth

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome – Paurush Praveen – Microbiome

The role of infection in miscarriage – Sevi Giakoumelou – Human Reproduction Update

Human gut microbiome

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial – Bumjo Oh – Helicobacter

Intestinal microbial communities associated with acute enteric infections and disease recovery – Pallavi Singh – Microbiome

Review: Advancing gut microbiome research using cultivation – Morten OA Sommer – Current Opinion in Microbiology

Human urinary tract microbiome

Re: The Microbiome of the Urinary Tract—A Role Beyond Infection – Alan J. Wein – The Journal of Urology

Animal models

Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats – Xu Zhang – Scientific Reports

A small-molecule antivirulence agent for treating Clostridium difficile infection – Kristina Oresic Bender – Science Translational Medicine

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel – Neelendu Dey – Cell

Animal microbiome

High-throughput DNA sequencing of the moose rumen from different geographical
location reveals a core ruminal methanogenic archaeal diversity and a differential
ciliate protozoal diversity – Suzanne Lynn Ishaq – Microbial Genomics

Microbial populations and fermentation profiles in rumen liquid and solids of Holstein cows respond differently to dietary barley processing – Barbara U. Metzler-Zebeli – Journal of Applied Microbiology

Culture based: Actinomycetes from the South China Sea sponges: isolation, diversity and potential for aromatic polyketides discovery – Zhiyong Li – Frontiers in Microbiology

Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig – Mackenzie Jonathan Slifierz – BMC Microbiology

Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission – Cristina Rodriguez – BMC Microbiology

Essential Amino Acid Supplementation by Gut Microbes of a Wood-Feeding Cerambycid – Paul A. Ayayee – Environmental Entomology

Plant, root, and soil microbiome

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere – Kalyan Chakravarthy Mynampati – Environmental Pollution

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features – Kayla N. Burns – Soil Biology and Biochemistry

Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes – Muhammad Saleem – Plant Microbe Interactions

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling – Feng Wang – Scientific Reports

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa – Anna Muratova – Journal of Plant Physiology

Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests – Naohiko T. Miyashita – Genes & Genetic Systems

Review: Ecological importance of soil bacterivores for ecosystem functions – Jean Trap – Plant and Soil

Editorial: Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Waste microbiology

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site – Lora R. McGuinness – PLOS ONE

Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Built environment microbiome

Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan – Aspen T Reese – ISME Journal

Microbiome of death

The Search for a Volatile Human Specific Marker in the Decomposition Process – E. Rosier – PLOS ONE

Bioinformatics and metagenomics

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database – Calum J. Walsh – BMC Microbiology

PhD thesis: Novel methods for comparing and evaluating single and metagenomic assemblies – Christopher M. Hill – University of Maryland

Microbes in the news

Metagenomic Sequencing Shows Changes in Healthy Gut Microbiome Pre- and Post-Antibiotics – Genome Web

Study shows whale microbiome shares characteristics with both ruminants and predators – Phys.org

Researchers isolate the ‘human smell of death’ – Elizabeth Pennisi – Science

Scientists find way to disarm deadly bacteria without destroying the good ones in your gut – Lena H. Sun – Washington Post

Science, publishing, and career

Failure to replicate the STAP cell phenomenon – Alejandro De Los Angeles – @nature

Make academic job advertisements fair to all: Too many university posts are given to men without proper competition – Mathias Wullum Nielsen – Nature

Gender-disparity study faces attack: A paper suggesting a Dutch grant scheme shows bias against women is criticized for a statistical flaw – Chris Woolston

Bik’s Picks

In the name of beauty: phasing out plastic microbeads found in skin scrubs – Nature

How Climate Change Shrank the Tongues of Long-Tongued Bumblebees – Ed Yong

Enamel evolved in the skin and colonized the teeth much later – EurekAlert

Giant Killer Lizards Lived Among Ice-Age Aussies – Discovery
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August 27, 2015

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Microbiome general/other

A comprehensive repertoire of prokaryotic species identified in human beings – Perrine Hugon – The Lancet Infectious Diseases

Linking the relevance of microbiota composition shifts with intestinal health disorders: a complex issue – Filip Boyen – Veterinary Journal

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes – Shira R. Abeles – PLOS ONE

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis– Aicui Liu – Drug Des Devel Ther

Pregnancy and birth microbiome

Several abstracts in Placenta:

 

Human oral microbiome

Pyrosequencing analysis of apical microbiota of teeth with persistent apical periodontitis – Yifan Ping – Journal of Dental Sciences

Human gut microbiome

Structure and function of the healthy pre-adolescent pediatric gut microbiome – Emily B. Hollister – Microbiome

Are proton pump inhibitors affecting intestinal microbiota health? – S. Melgar – Gastroenterology

Microbiome models

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling – Robert Caesar – Cell Metabolism

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development – Adam R Burns – The ISME Journal

Animal microbiome

The microbial community structure of the cotton rat nose – Diego Chaves-Moreno – Environmental Microbiology Reports

Water / Extremophile microbiome

Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs – Robert M.L. McKay – Environmental Microbiology Reports

High protists diversity in the plankton of sulfurous lakes and lagoons examined by 18s rRNA gene sequence analyses – Xavier Triadó-Margarit – Environmental Microbiology Reports

Bioreactor microbiology

Housefly Larvae Vermicomposting Efficiently Attenuates Antibiotic Resistant Genes in Swine Manure Coupled with Distinct Bacterial Population Change – Hang Wang – Applied and Environmental Microbiology

Techniques

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing – Wenke Smets – PeerJ PrePrints

Mock communities highlight the diversity of host-associated eukaryotes – Laura Wegener Parfrey – Molecular Ecology

Microbes in the news

Lab experiments question popular measure of ancient ocean temperatures – Hannah Hickey – University of Washington

Is your spacecraft contaminating the universe? – Jonathan Eisen – Microbe.net

Birmingham Zoo closes aviary after bacteria found in bird – Washington Times

Science, publishing, and career

EntryPoint! places students with disabilities on STEM tracks – Becky Ham – Science

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August 14, 2015

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Two papers on detection of bacteria in blood, vaginal microbiome, a discussion on eukaryotes in the human gut, and fungal communities’ resistance and resilience to wild fires. And some extra non-microbial Bik’s Picks for the weekend!

Human blood / infection microbiome

Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing – Peter Gyarmati – PLOS ONE

16S rRNA Gene Sequence-Based Identification of Bacteria in Automatically Incubated Blood Culture Materials from Tropical Sub-Saharan Africa – Hagen Frickmann – PLOS ONE

Human vaginal microbiome

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types – Arianne Y. K. Albert – PLOS ONE

Human gut microbiome

Are Human Intestinal Eukaryotes Beneficial or Commensals? – Julius Lukeš – PLOS Pathogens

Review: Role of the normal gut microbiota – Sai Manasa Jandhyala – World Journal of Gastroenterology

Review: Paleolithic nutrition for metabolic syndrome: systematic review and meta-analysis – Eric W Manheimer – The American Journal of Clinical Nutrition

Animal models

In Mice: Autophagy Protects against Colitis by the Maintenance of Normal Gut Microflora and Secretion of Mucus – Koichiro Tsuboi – Journal of Biological Chemistry

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance – Xingjia Xiang – Plant and Soil

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization – Xiaofang Li – Scientific Reports

Water microbiome

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary – Rachel L. Spietz – PLOS ONE

Techniques

Collection media and delayed freezing effects on microbial composition of human stool – Roberto Flores – Microbiome

Bioinformatics

Sorting out viral dark matter – Denise Waldron – Nature Reviews Microbiology

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction – Jonas Paulsen – PLOS Computational Biology

Other microbiology

Mycobacterium tuberculosis: Genome watch: Looking at Beijing’s skyline – Dorota Jamrozy & Teemu Kallonen – Nature Reviews Microbiology

Microbes in the news

Feeding My Curiosity – And My Microbes – Alanna Collen – uBiome

Crohn’s and Colitis video featuring Laboratory of Will DePaolo

Bik’s Picks – some extra for you for the weekend!

We’ve Used Up Our Annual Supply of Earth’s Resources—And It’s Only August – Maddie Stone – Gizmodo

Drones could be stressing out wildlife, scientists suggest – Chelsea Harvey – Washington Post

Low-fat diets ‘better than cutting carbs’ for weight loss – James Gallagher – BBC News

Google’s Life Sciences division to build a miniature glucose tracker – Mona Lalwani – EnGadget

Why scientists got an alligator to inhale helium – Rachel Feltman – Washington Post

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