October 8, 2015

Typo in title, some plagiarized text, and poor English but still including here: Metagenomic Human Repiratory Air in a Hospital Environment – Yi Yu Lai – PLOS ONE

Food microbiology

Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs – Emilie Lhomme – International Journal of Food Microbiology

Waste microbiology

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry – Priyanka Kumari – PLOS ONE

Phages and viruses

Mammalian Host-Versus-Phage immune response determines phage fate in vivo – Katarzyna Hodyra-Stefaniak – Scientific Reports

Microbial Ecology

Review: Microbiomes: unifying animal and plant systems through the lens of community ecology theory – Natalie Christian – Frontiers in Microbiology

Metagenomics and bioinformatics

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes
Sarah Temmam – PLOS ONE

Microbes in the news

“revolutionary poop platform”: Biomiic’s Platform Will Give People Microbiome Data From Crap: How Joseph Moon, Koji Yasuda and Soohong Kim are changing genomics Harvard iLab – Bostinno

Get To Know Your Poop Bacteria With This New iPhone App – Stephanie M. Lee – BuzzFeed

Could This Tough Bacteria Survive on Mars? – Irene Klot – Discovery

Bacteria in the world’s oceans produce millions of tonnes of hydrocarbons each year – Phys.org

Archaea: A headline on the front page of the New York Times for November 3, 1977, read “Scientists Discover a Way of Life That Predates Higher Organisms”. – Laura Eme, W. Ford Doolittle – Current Biology

The science of retweets – Science Daily
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October 5, 2015

Posted on October 5, 2015 by eliesbik

Characterizing and classifying the oral microbiome, homeostasis in the lung microbiome, collecting airborne microbes, and earthworms feeding on microbiomes.

Human oral microbiome

An accurate and efficient experimental approach for characterization of the complex oral microbiota – Wei Zheng – Microbiome

Phylogenetic approaches to microbial community classification – Jie Ning and Robert G. Beiko – Microbiome

DGGE: Stability of saliva microbiota during moderate consumption of red wine – Elvira Barroso – Archives of Oral Biology

Human respiratory tract microbiome

Review: Homeostasis and its Disruption in the Lung Microbiome – Robert P. Dickson – Am J Physiol Lung Cell Mol Physiol

Human gut microbiome

Faecalibacterium prausnitzii subspecies–level dysbiosis in the human gut microbiome underlying atopic dermatitis – Han Song – Journal of Allergy and Clinical Immunology

Animal models

Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4 – Barbara U. Metzler-Zebeli – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Waste treatment microbiology

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures – Manuel Aira – FEMS Microbiology Ecology

Food microbiology

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques – Mia Ryssel – International Journal of Food Microbiology

Air / Built environment microbiome

Passive dust collectors for assessing airborne microbial material – Rachel I. Adams – Microbiome

Microbes in the news

Beating parasites wins three scientists Nobel prize for medicine: “I think the microbes might almost deserve it more than I do” – Reuters

Nobel Prize Doctors still spreading word of bacteria find – Cathy O’Leary – The West Australian

Intrapartum antibiotics associated with altered infant gut microbiome – Maren Shapiro and Leah Bressler – 2MinuteMedicine

L’eau de bacteria: A whiff of the future? Biotech firms explore using microorganisms to produce flavors, fragrances – Benjamin Plackett – The Charlotte Observer

uBiome Co-Founder Jessica Richman Scoops Top Prize At IVY Awards, uBiome Is Finalist In MedTech Innovator of 2015 – PR Web

Podcast: Our microbiome and our health. Guests: Gary Wu, Tracy Bale, Frederic Bushman – RadioTimes

Microbiome Monday: Animals and Their BFFs – American Museum of Natural History

Permafrost-eating bacteria: a new twist on thawing Arctic and global warming – Thomas S Bianchi – The Conversation

Microbes may play a major role in cloud formation and wet weather – Richard Gray – Daily Mail

Volkswagen: Diesel transplants reveal likely culprit behind DeiselGate: car microbiomes -featuring Jeferina Gordon, Josephine Candelsman, and Hands Dieter Poetsch – – Morten Blaser – The Megabiome

Bacteria Hysteria

Take care when reusing bags: Reusing carrier bags for a diverse range of contents puts consumers at risk of bacterial contamination – Worthing Herald

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October 4, 2015

Posted on October 4, 2015 by eliesbik

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

Posted on October 1, 2015 by eliesbik

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 29, 2015

Posted on September 29, 2015 by eliesbik

Gut microbiota in first year of life, the mouse gut metagenome, microbiome and metabolome of cats and dogs, and lichen and flea microbes found in amber.

Pregnancy and birth

Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study – MB Azad – BJOG: An International Journal of Obstetrics & Gynaecology

Human oral microbiome

Oral Microbiome in Chinese Patients with Aggressive Periodontitis and Their Family Members – Yi Li – Journal of Clinical Periodontology

Characterizing Diversity of Lactobacilli Associated with Severe Early Childhood Caries: A Study Protocol – Yihong Li – Advances in Microbiology

Human gut microbiome

Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire: a proof-of-concept study – Pierre H.H. Schneeberger – Infection, Genetics and Evolution

Editorial: Rifaximin, a Molecule with Newly Discovered Anti-inflammatory Properties May Help Shaping the Microbiome and Its Interaction with Host Immunity – F. Pandolfi – Mini-Reviews in Medicinal Chemistry

PhD Thesis: A Computational Tool for Investigating Mechanistic Relationships in the Colon-Diet-Flora Complex – Arun S. Moorthy – University of Guelph

Animal models

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells – Koji Atarashi – Cell

Research Highlights: Keeping track of gut bacteria – Irene Jarchum – Nature Methods

Animal microbiome

A catalog of the mouse gut metagenome – Liang Xiao – Nature Biotechnology

Keynote presentation: The importance of the microbiome and metabolome in health and disease of dogs and cats – Jan Suchodolski – Acta Veterinaria Scandinavica

Antimicrobial use in swine production and its effect on the swine gut microbiota and antimicrobial resistance – Devin B. Holman – Canadian Journal of Microbiology

Pathogen Loading From Canada Geese Faeces in Freshwater: Potential Risks to Human Health Through Recreational Water Exposure – T. J. Gorham – Zoonoses and Public Health

Review: Coral – The World’s Most Diverse Symbiotic Ecosystem – Linda L. Blackall – Molecular Ecology

New Brazilian giant viruses isolation from environmental samples using a panel of protozoa – Fábio P. Dornas – Frontiers in Microbiology

A New Genus of Fleas with Associated Microorganisms in Dominican Amber – George Poinar Jr. – Journal of Medical Entomology

Isolation and Identification of Pathogenic Filamentous Fungi and Yeasts From Adult House Fly (Diptera: Muscidae) Captured From the Hospital Environments in Ahvaz City, Southwestern Iran – Hamid Kassiri – Journal of Medical Entomology

Plant, root, and soil microbiome

Mycorrhizal diversity, seed germination and long-term changes in population size across nine populations of the terrestrial orchid Neottia ovata – Hans Jacquemyn – Molecular Ecology

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) – Nicolas Delhomme – PLOS ONE

Order of arrival structures arbuscular mycorrhizal colonization of plants – Gijsbert D. A. Werner – New Phytologist

Elevated atmospheric CO2 increases microbial growth rates in soil: results of three CO2 enrichment experiments – Evgenia Blagodatskaya – Global Change Biology

Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds – Vívian N. Gonçalves – Environmental Microbiology

The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression – Manuela Krüger – Molecular Ecology

Lichen-associated fungi from Paleogene amber – Elina Kettunen – New Phytologist

Changes in soil bacterial communities and diversity in response to long-term silver exposure – Sotirios Vasileiadis – FEMS Microbiology Ecology

Review: Diversity, distribution and biotechnological potential of endophytic fungi – You-Kun Zheng – Annals of Microbiology

Water microbiome

Assessment of microbial populations within Chicago area nearshore waters and interfaces with river systems – Emily Sible – Data in Brief

Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River – Mariya W. Smith – Frontiers in Microbiology

Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs – Beth H. Baker – Water Research

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments – Dong Li – Environmental Microbiology

Bacterial community shift drives antibiotic resistance promotion during drinking water chlorination – Shuyu Jia – Environmental Science & Technology

Waste microbiology

The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters – Junpeng Rui – Biotechnology for Biofuels

Microbial Ecology

Interspecific diversity reduces and functionally substitutes for intraspecific variation in biofilm communities – Kai Wei Kelvin Lee – The ISME Journal

Bioinformatics

MG7: Configurable and scalable 16S metagenomics data analysis – Alexey Alekhin – BioRxiv

Robust Parameter Estimation for Biological Systems: A Study on the Dynamics of Microbial Communities – Matthias Chung – ArXiv

Techniques

Review: Contemporary molecular tools in microbial ecology and their application to advancing biotechnology – Mamoon Rashid – Biotechnology Advances

Microbes in the news

In intro biology lab, students become research subjects – Julia Liss – Michigan Daily

β-glucan-enriched Pasta Boosts Good Gut Bacteria, Reduces Bad Cholesterol – Science 2.0

Two medical students hope to treat superbug with donations to their ‘poo bank’ – Western Daily Press

Bacteria in ancient flea may be ancestor of the Black Death: Plague bacteria may be 20 million years old– Oregon State University

Antarctic bacteria could hold secret to finding life on Mars – University of Tasmania
[hr]

September 27, 2015

Posted on September 27, 2015 by eliesbik

General microbiome

Power Law Analysis of the Human Microbiome – Zhanshan Sam Ma – Molecular Ecology

Pregnancy and birth

Review: Probiotics and necrotizing enterocolitis – Paul Fleming – Pediatric Surgery International

Human oral microbiome

The efficacy of two oral hygiene regimens in reducing oral malodour: a randomised clinical trial – Magda Feres – International Dental Journal

Human respiratory tract microbiome

PhD Thesis: Investigating the host and bacterial factors in cystic fibrosis that promote persistence of infection in the lung – Daniel James Smith – University of Queensland

Human gut microbiome

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants – Roberto Berni Canani – The ISME Journal

Review: Reciprocal interaction of diet and microbiome in inflammatory bowel diseases – Monika Schaubeck – Current Opinion in Gastroenterology

Review: Resistant starches for the management of metabolic diseases – Laure B. Bindels – Current Opinion in Clinical Nutrition & Metabolic Care

Animal models

Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna – Martijn Callens – The ISME Journal

Animal microbiome

Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption – J. Stoops – Food Microbiology

Indigenous microbiota and Leishmaniasis – Mateus Eustáquio de Moura Lopes – Parasite Immunology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B Hadapad – Pest Management Science

Plant, root, and soil microbiome

Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes – Fabiola Miranda-Sánchez – Environmental Microbiology

Non-random species loss in bacterial communities reduces antifungal volatile production – W. H. Gera Hol – Ecology

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment – Mohammad Bahram – The ISME Journal

Plant and root-endophyte assembly history: interactive effects on native and exotic plants – Benjamin A. Sikes – Ecology

Review: Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach – Fernando Carlos Gómez-Merino – Acta Physiologiae Plantarum

Review: Engineering Microbiomes to Improve Plant and Animal Health – U.G. Mueller – Trends in Microbiology

Water microbiome

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River – Bonnie L. Brown – Standards in Genomic Sciences

Extremophile microbiome

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy – Judith M Klatt – The ISME Journal

Emerging spatial patterns in Antarctic prokaryotes – Chun Wie Chong – Frontiers in Microbiology

Waste microbiology

Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels – Maria Westerholm- Biotechnology for Biofuels

Food microbiology

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing – Ruo-si Fang – Journal of Food Sciences

Isolation and characterization of bacteriocinogenic lactic bacteria from M-Tuba and Tepache, two traditional fermented beverages in México – Norma M. de la Fuente-Salcido – Food Science & Nutrition

Built environment microbiology

Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel – Nahum Y. Shpigel – PLOS ONE

Microbial Ecology

Transient dynamics of competitive exclusion in microbial communities – Stilianos Louca – Environmental Microbiology

Metagenomics and bioinformatics

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens – Bastian Greshake – Molecular Ecology Resources

Review: Recovering full-length viral genomes from metagenomes – Saskia Smits – Frontiers in Microbiology

Editorial: The main challenges that remain in applying high-throughput sequencing to clinical diagnostics – Michael Loeffelholz & Yuriy Fofanov – Expert Review of Molecular Diagnostics

Microbes in the News

uBiome Supports Oral Disease Prevention with Donations and Study – PR Web

Probiotic Formula Reverses Cow’s Milk Allergies by Changing Gut Bacteria of Infants – Lab Manager

Microbes and art

Microbe artwork shows the limits of antibiotics – University of Oxford

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September 25, 2015

Posted on September 25, 2015 by eliesbik

A crowd funding project to study mind and microbes, impact of early life gut colonization, microbial aspect to terroir, and khmer sequence analysis.

Crowd funding project: Are our bacteria making us depressed or anxious? – Philip Strandwitz – Experiment.com

Pregnancy and birth

Review: The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us? – J. G. Wallace – Journal of Developmental Origins of Health and Disease

Human gut microbiome

Chronic Kidney Disease: The Influence of CKD on Colonic Microbial Metabolism – Ruben Poesen – Journal of the American Society of Nephrology

Review: Could the beneficial effects of dietary calcium on obesity and diabetes control be mediated by changes in intestinal microbiota and integrity? – J. M. G. Gomes – British Journal of Nutrition

Animal models

The microbiota shifts the iron sensing of intestinal cells – Jean-Christophe Deschemin – The FASEB Journal

Plant, root, and soil microbiome

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health – Zhong Wei – Nature Communications

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir – Sarah Knight – Scientific Reports

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil – Souichiro Kato – Scientific Reports

Food microbiology

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil
A.A.M. De-Melo – Letters in Applied Microbiology

Waste microbiology

The biotransformation of brewer’s spent grain into biogas by anaerobic microbial communities – Dina V. Malakhova – World Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

The khmer software package: enabling efficient nucleotide sequence analysis – Michael R. Crusoe – F1000 research

Microbes in the news

That Stinky Cheese Is a Result of Evolutionary Overdrive – Carl Zimmer – New York Times

Bacteria are making it harder for would-be murderers – Alexandra Petri – Washington Post

Bacteria Hysteria

Note: research sponsored by Dettol: How your child’s teddy could trigger food poisoning: 80% of cuddly toys harbour harmful bacteria – while one in four are contaminated with faeces – Lizzie Parry – Daily Mail

Science, publishing, and career

How science fairs shaped my career – Rachel Yoho – Science

Bik’s Picks

Scientists discover new system for human genome editing – Phys.org

The truth about pigs – Henry Nicholls – BBC

1 1/2-pound baby born to Utah woman on cruise ship beats odds to survive – Lindsey Whitehurst – Associated Press
[hr]

September 24, 2015

Posted on September 24, 2015 by eliesbik

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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September 22, 2015

Posted on September 22, 2015 by eliesbik

Effect of hookworm infection on microbiome of celiac subjects, neutrophil ageing, altering the bone niche, and a personal microbial cloud.

Pregnancy and birth

Influence of a combination of probiotics on bacterial infections in very low birthweight newborns – Zlatka Kanic – Wiener klinische Wochenschrift

Microbiome of death

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses – Seung Hak Yang – Genetics and Molecular Biology

Human respiratory tract microbiome

Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics – Leah J. Hauser – International Forum of Allergy & Rhinology

Human oral microbiome

Comparison of Subgingival and Peri-implant Microbiome in Chronic Periodontitis – Zhang, Qian – Chinese Journal of Dental Research

The novel association between red complex of oral microbe and body mass index in healthy Japanese: a population based cross-sectional study – Kanae Matsushita – Journal of Clinical Biochemistry and Nutrition

Human gut microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects – I. Rangel – Alimentary Pharmacology & Therapeutics

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial – Hyuk Yoon – Journal of Clinical Biochemistry and Nutrition

Review: Improving healthspan via changes in gut microbiota and fermentation – Michael J. Keenan – AGE

Review: Gastric Microbiota – Gianluca Ianiro – Helicobacter

Thesis: High-resolution analysis of the human intestinal microbiota stability landscape – Tineka Blake – Aalto University

Animal models

An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea – Yemeng Li – RCS Advances

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche – Yubin Luo – Cell Metabolism

The levonorgestrel-releasing intrauterine system is associated with delayed endocervical clearance of Chlamydia trachomatis without alterations in vaginal microbiota – E.R. Liechty – Pathogens and Disease

Goldfish: Correlations of Gut Microbial Community Shift with Hepatic Damages and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure – Haifeng Kan – Environmental Science & Technology

Neutrophil ageing is regulated by the microbiome – Dachuan Zhang – Nature

Animal microbiome

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea – Qingsong Yang – Aquatic Ecosystem Health & Management

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease – Ermanno Federici – Microbes and Environments

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression –
Jia Y. Har – Frontiers in Microbiology

Plant, root, and soil microbiome

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage – Natalia Pimentel Esposito-Polesi – World Journal of Microbiology and Biotechnology

Endospores, prokaryotes, and microbial indicators in arable soils from three long-term experiments – Paulina Tamez-Hidalgo – Biology and Fertility of Soils

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities – Sandra Ronca – Frontiers in Microbiology

Responses of aromatic-degrading microbial communities to elevated nitrate in sediments –
Meiying Xu – Environmental Science & Technology

Climate change and physical disturbance cause similar community shifts in biological soil crusts – Scott Ferrenberg – PNAS

Water / Extremophile microbiome

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing – Jae-Ho Jung – Animal Cells and Systems

Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing – H. Jing – Biogeosciences Discussions

Built environment microbiome

Humans differ in their personal microbial cloud – James F. Meadow – PeerJ

Waste microbiology

Relationship between bacterial diversity and environmental parameters during composting of different raw materials – Xueqin Wang – Bioresource Technology

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination – Siobhan O’Brien, Angus Buckling – EMBO Reports

Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation – Marc A. Demeter – Frontiers in Microbiology

Microbial Ecology

Predicting microbial traits with phylogenies – Marta Goberna and Miguel Verdú – The ISME Journal

Bioinformatics and metagenomics

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories – Christine L Sun – The ISME Journal

CCLasso: correlation inference for compositional data through Lasso – Huaying Fang – Bioinformatics

Computational methodology for predicting the landscape of the human–microbial interactome region level influence – Edgar D. Coelho – Journal of Bioinformatics and Computational Biology

Techniques

Targeted single molecule mutation detection with massively parallel sequencing – Mark T. Gregory – Nucleic Acids Research

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures – Stefan A. Boers – Scientific Reports

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis – Thomas Briese – mBio

Microbes in the news

Wherever You Go, Your Personal Cloud Of Microbes Follows – Rob Stein – NPR

Former CEO knew about contamination, wrote “Just ship it”: 28 years for salmonella: Peanut exec gets groundbreaking sentence – Moni Basu – CNN

UGA microbiology researchers identify potential mechanism for neurodegenerative diseases – News Medical

Researchers find novel signature in the brains of children with cerebral malaria – EurekAlert

Science, publishing, and career

About annoying invitations to write papers in questionable journals and strategies how to handle those: You are invited to submit… – David Moher and Anubhav Srivastava – BMC Medicine

Bik’s Picks

8 trillion microbeads pollute U.S. aquatic habitats daily – Jareen Imam – CNN

Science Says This Is the Sound Giraffes Make – Alexandra Sifferlin – Time

I Am the Walrus: What 35,000 Walruses Tell Us About Our Future in Warming World – Miyoko Sakashita – Huffington Post

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Waste and pollution

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