Category Archives: Animal experiments

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 30, 2015

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Gut virome in infants, metabolome of Mediterranean diet, zebrafish gut assembly, antibiotic use and psoriasis risk, Roseobacter proteomics, and MetaPhlAn2.

Pregnancy and birth

The gut virome and bacterial microbiome—the early years – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Early life dynamics of the human gut virome and bacterial microbiome in infants –
Efrem S Lim – Nature Medicine

Human oral microbiome

Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis – Szymon P Szafrański – NPJ Biofilms and Microbiomes

Urease and Dental Plaque Microbial Profiles in Children – Evangelia Morou-Bermudez – PLOS ONE

High prevalence of colonization of oral cavity by respiratory pathogens in frail older patients with oropharyngeal dysphagia – O. Ortega – Neurogastroenterology & Motility

Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance – Ana Paula Vieira Colombo – Microbial Pathogenesis

Human gut microbiome

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome – Francesca De Fillippis – Gut

Review: Clinical and Pathophysiological Consequences of Alterations in the Microbiome in Cirrhosis – Jane Macnaughtan – American Journal of Gastroenterology

Animal models

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut – Sandi Wong – mBio

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis –
Peter Zanvit – Nature Communications

Plant, root, and soil microbiome

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Oily waste containing natural radionuclides: does it cause stimulation or inhibition of soil bacterial community? – Polina Galitskaya – Journal of Plant Nutrition and Soil Science

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Water microbiome

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

Extremophile microbiome

Perspective: The discovery of Antarctic RNA viruses: a new game changer – Ricardo Cavicchioli – Molecular Ecology

Metagenomics and bioinformatics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling – Duy Tin Truong – Nature Methods

Metabolomics, proteomics

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products – Chad W. Johnston – Nature Communications

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

CRISPRs

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins – Joseph Bondy-Denomy – Nature

Review: CRISPR-Cas immunity in prokaryotes – Luciano A. Marraffini – Nature

Microbes in the news

Study Links Skin Microbiome to Infections – Skin Inc

Ancient ‘Superman’ microbe’s ability to withstand damage to its DNA could be key to unlocking cancer cure, Chinese scientists say – Stephen Chen – South China Morning Post

Another Frontier in Microbiome Research: Preterm Birth – Julie A. Jacob – JAMA

Science, publishing, and career

A taxonomy of authorship roles – Credit Casrai

Bik’s Picks

What if everyone lived to 100? – Georgina Peters – London Business School Review

Gene-Edited “Micropigs” to Be Sold as Pets: The institute in Shenzhen, China, that creates the pigs quoted an initial price tag of $1,600 – David Cyranoski – Scientific American / Nature

1500-Year-Old Mosaic Map Found – Rossella Lorenzi – Discovery

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September 29, 2015

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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
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September 27, 2015

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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 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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September 23, 2015

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Animal models

In mice: The outer mucus layer hosts a distinct intestinal microbial niche – Hai Li – Nature Communications

Animal microbiome

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores – Jon G. Sanders – Nature Communications

Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata – Amanda Shore-Maggio – Applied and Environmental Microbiology

Macaque feces: Non-random patterns in viral diversity – Simon J. Anthony – Nature Communications

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome – Pia H. Moisander – PLOS ONE

Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA – Yang Xiang – PLOS ONE

Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species – Mark W. Eshoo – PLOS ONE

Plant, root, and soil microbiome

Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors – Madhav Prakash Thakur – Global Change Biology

Trait-based partner selection drives mycorrhizal network assembly – Pierre-Luc Chagnon – Oikos

Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi – Wietse de Boer – PLOS ONE

Exometabolite niche partitioning among sympatric soil bacteria – Richard Baran – Nature Communications

Water microbiome

The dynamical landscape of marine phytoplankton diversity – Marina Lévy – Journal of the Royal Society/Interface

Bioinformatics

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments – Constantinos Tsirogiannis and Brody Sandel – Ecography

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data – Simon H. Tausch – PLOS ONE

Microbes in the news

You Produce a Microbial Cloud That Can Act Like an Invisible Fingerprint – Brian Handwerk – Smithsonian

Baleen Whale Shares Gut Microbiome Features with Land Herbivores, Carnivores – Genome Web

Bacteria Turns Santa Barbara Bird Refuge Pink – Alys Martinez – KEYT.com

Microbiome Diversity Affects Chemotherapy-Related Infection – Kate Johnson – Medscape

NASA’s Human Research Program studies how Microbes interact with Astronauts during Spaceflight – Amy Blanchett and Laurie Abadie – NASA

Stanford team re-engineers virus to deliver therapies to cells – Tom Abate – Stanford News

Science, publishing, and career

Four Proposals to Help Improve the Medical Research Literature – David Moher , Douglas G. Altman – PLOS Medicine

Gender contributes to personal research funding success in The Netherlands – Romy van der Lee and Naomi Ellemers – PNAS

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September 22, 2015

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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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September 5, 2015

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Events

The Individual Microbe: Single-cell Analysis and Agent-based Modeling – ASM conference – March 18-20, 2016, Washington DC, USA

R workshop for microbial ecology – Pat Schloss – Nov 2-4, 2015, Detroit – No link but can email Pat at: pschloss@umich.edu

General microbiome

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – BioRxiv

Pregnancy and birth microbiome

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development – Federica Del Chierico – PLOS ONE

Human oral microbiome

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial – Jessica E. Koopman – PLOS ONE

Review: Oral Paleomicrobiology: study of the ancient oral microbiome – Namrata Dagli

Human gut microbiome

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children – M. Isabel Ordiz – Microbiome

Gastrointestinal Microbiome Modulator Improves Glucose Tolerance in Overweight and Obese Subjects: A Randomized Controlled Pilot Trial – Candida J. Rebello – Journal of Diabetes and its Complications

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis – Griet Debyser – Journal of Cystic Fibrosis

Review: Pathways and functions of gut microbiota metabolism impacting host physiology – Smitha Krishnan – Current Opinion in Biotechnology

Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases – Jose U. Scher – Arthritis & Rheumatology

Review: The human microbiome: opportunities and challenges for clinical care – G. B. Rogers – Internal Medicine Journal

Human respiratory microbiome (see also gut microbiome above)

MRSA Colonization and the Nasal Microbiome in Adults at High Risk for Colonization and Infection – Mary T. Bessesen – Journal of Infection

Review: Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection – Lindsay J. Caverly – Pediatric Pulmonology

Human other sites

In silico analyses of metagenomes from human atherosclerotic plaque samples – Suparna Mitra – Microbiome

Microbiome models

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Perspective: Metabolic labeling puts the microbiome under the microscope – Graham J Britton & Jeremiah J Faith – Nature Medicine

Animal microbiome

The composition of the zebrafish intestinal microbial community varies across development – W Zac Stephens – ISME Journal

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season – Jane Ludvigsen – Microbes and Environments

The genome of Aiptasia, a sea anemone model for coral symbiosis – Sebastian Baumgarten – PNAS

Special Issue: The Mammalian Microbiome and Its Importance in Laboratory Animal Research – André Bleich and James G. Fox – ILAR Journal

Plant, root, and soil microbiome

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling – Peter E. Larsen – PLOS ONE

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential – Asma Soussi – Plant and Soil

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Water microbiome

Anthropogenic activities drive the microbial community and its function in urban river sediment – Xu Zhang – Journal of Soils and Sediments

Built environment microbiome

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – Journal of Medical Entomology

Hospital’s Hidden Environmental Hazards: Probing the Microbiome – BioScience

Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China – Hongxing Ren – Applied Microbiology and Biotechnology

Food microbiology

The genomics of microbial domestication in the fermented food environment –
John G Gibbons – Current Opinion in Genetics & Development

Bioinformatics

Functional Basis of Microorganism Classification – Chengsheng Zhu – PLOS Computational Biology

ReproPhylo: An Environment for Reproducible Phylogenomics – Amir Szitenberg – PLOS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities – Dongwan D. Kang – PeerJ

More Microbiology

Evolution of coexistence in a crowded microplate well – J. Arjan G. M. de Visser – PNAS

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities – Tomáš Větrovský – Molecular Ecology Resources

Microbes in the news

Microbial diversity insights are often strongly biased – Suffield Times
Small advances: understanding the microbiome – Amanda Smith – ABC Australia

Science, publishing and career

When science fails a scientist – Kim Hunter-Schaedle – Science

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September 2, 2015

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I will be traveling in the next 2 weeks, so The Digest might not come out every day, but I will try to keep my best to post as often as I can. Also, NCBI’s PubMed email alerts have not been coming out daily in the last week, and when they arrive they contain 70+ papers. Today I did not get any, so I have a very small digest:

Pregnancy and birth

Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy – Saad S. Al-Shehri – PLOS ONE

Microbiome models

Exploitation of the Medfly Gut Microbiota for the Enhancement of Sterile Insect Technique: Use of Enterobacter sp. in Larval Diet-Based Probiotic Applications – Antonios A. Augustinos – PLOS ONE

Editorial: Lactobacillus acidophilus opens the door to butyrate – Gillian Patman – Nature Reviews Gastroenterology & Hepatology

Water microbiome

Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition – Gustavo Bueno Gregoracci – PLOS ONE

Microbes in the news

Mars Dome – a cool closed system – Alex Alexiev – MicroBEnet

Scientists Mimic Sharkskin to Develop Bacteria Resistant Surfaces – Ivan Budimir – NewsWire

Polio in two Ukrainian children first occurrence of disease in Europe since 2010 – Sarah Boseley – The Guardian

Science, publishing, and career

Funny: Fifth-Grade Science Paper Doesn’t Stand Up To Peer Review – the Onion

Bik’s Picks

Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences – Jennifer Hawkins – PLOS ONE

New Species of Ancient ‘River’ Dolphin Lived in the Ocean – Sara G. Miller – Live Science / Discovery

How America’s love affair with caffeine has sparked a crisis of overdoses — and what the FDA is trying to do about it – Ariana Eunjung Cha – Washington Post
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September 1, 2015

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General microbiome

Perspective: Better together: engineering and application of microbial symbioses – Stephanie G Hays – Current Opinion in Biotechnology

Pregnancy and birth

Maternal use of probiotics during pregnancy and effects on their offspring’s health in an unselected population – Nicole Rutten – European Journal of Pediatrics

Impact of maternal bifidobacteria and the mode of delivery on Bifidobacterium microbiota in infants – S. Sirilun – Beneficial Microbes

Human Milk Oligosaccharides in Premature Infants: Absorption, Excretion and Influence on the Intestinal Microbiota – Mark A. Underwood – Pediatric Research

The influence of impact delivery mode, lactation time, infant gender, maternal age and rural or urban life on total number of Lactobacillus in breast milk Isfahan – Iran – Mansoureh Taghizadeh – Advanced Biomedical Research

Review: Maternal Microbiome and Pregnancy Outcomes That Impact Infant Health: A Review – Anne L Dunlop – Advances in Neonatal Care

Human gut microbiome

Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis – Akiko Kinumaki – Frontiers in Microbiology

Review: Microbiome Disturbances and Autism Spectrum Disorders – Cheryl S. Rosenfeld – Drug Metabolism & Disposition

Review: Investigation of Host–Gut Microbiota Modulation of Therapeutic Outcome – Lian Yee Yip – Drug Metabolism & Disposition

Perspective: Could gut microbiota protect against sclerosing cholangitis? – Hanns-Ulrich Marschall – Hepatology

Models of microbiome research

Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community – Hirosuke Sugahara – Scientific Reports

Microbial community profiles of the colon from steers differing in feed efficiency – Phillip R Myer – Springer Plus

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene – G. Estruch – PLOS ONE

Lean rats gained more body weight than obese ones from a high-fibre diet – Shaoting Li – British Journal of Nutrition

Microbiota RORgulates intestinal suppressor T cells – Ahmed N. Hegazy – Science

Review: Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design – Debby Laukens – FEMS Microbiology Reviews

Animal microbiome

Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp – Andres Gomez – The ISME Journal

Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae – Kazunari Ushida – Animal Science Journal

Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata – Man Kit Cheung – Marine Biotechnology

Plant, root, and soil microbiome

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing – Wu Xiong – PLOS ONE

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust – Cara Magnabosco – The ISME Journal

A review: What is the spermosphere and how can it be studied? – Séverine Schiltz – Journal of Applied Microbiology

Metagenomics and bioinformatics

glmgraph: An R Package for Variable Selection and Predictive Modeling of Structured Genomic Data – Li Chen – Bioinformatics

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes – Kou-San Ju – PNAS

Techniques

Mass Spectrometry-based PhyloProteomics (MSPP): A novel microbial typing Method – Andreas Erich Zautner – Scientific Reports

Microbes and art

Made of Bacteria, This Living Type Morphs Into New Letterforms: Ori Elisar’s project Living Language blurs the lines between designer and mad scientist with his Hebrew symbols grown in petridishes – Meg Miller – FastcoDesign

Microbes in the news

Unusual throat (and mouth) germs linked to schizophrenia, says two new studies – Amy Ellis Nutt – Washington Post

Some Sexually Transmitted Microbes Might Be Good for You – Marissa Fessenden – Smithsonian

How Does Your Microbiome Grow? The reproduction rates of the bacteria in one’s gut may be a good indicator of health or disease – Health Canal

How Do We Build Our Microbiomes? Exhibition “The Secret World Inside You” opens November 7 – American Museum of Natural History

New Yeast And Bacterial Starters Developed For Truly Wild European Wines – Eurasia Review

Bacteria Hysteria

Are your kid’s backpacks a magnet for bacteria? – Anna Zook – WJHL.com

Bik’s Picks

Acoustic shadows help gleaning bats find prey, but may be defeated by prey acoustic camouflage on rough surfaces – Elizabeth L Clare – eLIFE
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