Category Archives: Microbial Ecology

October 20, 2015

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Cohabitation of helminths, bacteria, and host in the gut, diurnal sampling bias in plankton biodiversity, contaminant influence on groundwater microbiome, volatile affairs, and new tools for metagenomics.

Events

Postdoc and grad student Summit — preceding the EMBO Symposium on Aquatic Microeukaryotes: Abstract deadline October 22 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Periodontal clinical and microbiological characteristics in healthy versus generalized aggressive periodontitis families – Mabelle de F. Monteiro – Journal of Clinical Periodontology

Masters Thesis: Caries and the Oral Microbiome of a Native American Population – Michael Tuan – Ohio State University

Human gut microbiome

Review: Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity – Lisa A. Reynolds – The Journal of Immunology

Review: Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases – Bidisha Paul – Clinical Epigenetics

Review: Intestinal Microbiota Metabolism and Atherosclerosis – Tian-Xing Liu – Chinese Medical Journal

Animal models

Colonic Lesions, Cytokine Profiles, and Gut Microbiota in Plasminogen-Deficient Mice – Bill Vestergaard – Comparative Medicine

Plant, root, and soil microbiomes

Cyanobacterial composition and spatial distribution based on pyrosequencing data in the Gurbantunggut Desert, Northwestern China – Bingchang Zhang – Journal of Basic Microbiology

Disease in apple orchards: Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth? – Bunlong Yim – Frontiers in Microbiology

A fragrant neighborhood: Volatile mediated bacterial interactions in soil – Kristin Schulz-Bohm – Frontiers in Microbiology

Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing – Lin Chen – Frontiers in Microbiology

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California – A. C. Hollowell – Plant Microbe Interactions

Water microbiome

Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique – Satoshi Nagai – Gene

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations – Xiaofen Wu – The ISME Journal

Viral impact on prokaryotic and microalgal activities in the microphytobenthic biofilm of an intertidal mudflat (French Atlantic coast) – Hélène Montanié – Frontiers in Microbiology

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes – Christopher L. Hemme – Frontiers in Microbiology

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir – Xiao Yang – Water

Extremophile microbiology

Review: Extremely Thermophilic Microorganisms as Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals – Benjamin M. Zeldes – Frontiers in Microbiology

Metagenomics and bioinformatics

Snowball: Strain aware gene assembly of Metagenomes – I. Gregor – ArXiv

PEPR: Pipelines for Evaluating Prokaryotic References – Nathan D. Olson – PeerJ preprint

cual­id: globally unique, correctable, and human­friendly sample identifiers for
comparative ­omics studies – John H Chase – PeerJ preprint

Why we need more algal metagenomes – Linda E. Graham – Journal of Phycology

Phages and viruses

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters – Jeremy J. Barr – PNAS

Microbial Ecology

Interspecies interactions are an integral determinant of microbial community dynamics –
Fatma A. A. Aziz – Frontiers in Microbiology

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity – Caroline M. Tucker – Oikos

Review: Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review – Patricia M. C. Huijbers – Environmental Science & Technology

More microbiology

Self-Protected Nitrate Reducing Culture for Intrinsic Repair of Concrete Cracks –
Yusuf C. Ersan – Frontiers in Microbiology

Metabolomics

Review: Volatile affairs in microbial interactions – Ruth Schmidt – The ISME Journal

Microbes in the news

Society for Neuroscience meeting in Chicago : Probiotic bacteria may aid against anxiety and memory problems – Ian Sample – The Guardian

ID Week: How Babies’ Gut Bacteria May Help Find Treatments for C. Diff – Rachael Rettner – Live Science

Video: Speaking of Chemistry: What is the Gut Microbiome? Matt Davenport – American Chemical Society

Study reveals a key role your gut bacteria play in body’s self-defense – David Callahan – Medical Xpress

Gut Microbiome Insights; Obesity and Digestive Health Risks; Delivery Options and Predictors of Failure for Fecal Microbiota Transplantation; among Featured Topics Presented at the American College of Gastroenterology’s 80th Annual Meeting – PR NewsWire

MS conference, Barcelona: Q&A With Helen Tremlett From the University of British Columbia: Gut Microbiome And Its Role In Multiple Sclerosis -HCP Live

Virginia Tech scientists reveal more about how body copes with common gut bacterium – Augusta Free Press

High Starch Diets’ Effects on Stress Response in Horses – Casie Bazay – The Horse

These Bacteria Could Live in Europa’s Ocean – Irene Klotz – Discovery

Local news: Dozens Sick With Shigella Bacteria After Eating At San Jose Restaurant – CBS Local

The Phage is a Lonely Hunter: New research reveals that bacteriophages use slow, staccato movements to hunt bacteria on cell surfaces – Michael Price – SDSU

Creating Healthier Microbiomes, from Conception to Childhood: A Clinical Conversation with Geeta Maker-Clark, MD, and Robert Rountree, MD -Alternative and Complementary Therapies

Microbes and art

Very cool: A Microbiologist Recreated ‘Starry Night’ With Bacteria In A Petri Dish And it’s not too shabby – Priscilla Frank – Huffington Post

Bik’s Picks

Poo turns naked mole rats into better babysitters – Oestrogen in queen mole rat’s faeces drives subordinates to care for her pups – Sara Reardon – Nature News
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October 15, 2015

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Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyuan Fu – Circulation Research

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

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

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

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

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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October 13, 2015

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Tongue coating microbiota, fecal microbiota in Tibetan and Chinese Han, the gut mycobiome in obesity, and the Hoopoe’s uropygial gland.

Pregnancy and birth

Review: Neonatal Gut Microbiota and Human Milk Glycans Cooperate to Attenuate Infection and Inflammation – David S Newburg – Clinical Obstetrics & Gynecology

Research highlight: Early life dysbiosis increases asthma risk – Naomi Attar – Nature Reviews Microbiology

Review: Gut Microbiome and the Development of Food Allergy and Allergic Disease – Benjamin T. Prince – Pediatric Clinics of North America

Human oral microbiome

Variations of Tongue Coating Microbiota in Patients with Gastric Cancer – Jie Hu – BioMed Research International

Review: Microbial Nucleic Acid Sensing in Oral and Systemic Diseases – K.E. Crump – Journal of Dental Research

Human respiratory microbiome

Review: The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection – Alexander J. Adami – Tuberculosis

Human gut microbiome

Comparative analyses of fecal microbiota in Tibetan and Chinese Han living at low or high altitude by barcoded 454 pyrosequencing – Long Li & Xin Zhao – Scientific Reports

Obesity changes the human gut mycobiome – M. Mar Rodríguez – Scientific Reports

Review: Understanding Luminal Microorganisms and Their Potential Effectiveness in Treating Intestinal Inflammation – Ince, M. Nedim – Inflammatory Bowel Diseases

Review: Brain-gut-microbiota axis in Parkinson’s disease – Agata Mulak, Bruno Bonaz – World Journal of Gastroenterology

Research Highlight: In transit – Denise Waldron – Nature Reviews Microbiology

Review: Gut microbiota and non-alcoholic fatty liver disease [PDF]-  Paraskevas Gkolfakis – Hepatobiliary Pancreat Dis Int

Animal microbiome

The Hoopoe’s Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird – Sonia M. Rodríguez-Ruano – PLOS ONE

Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus – E. Jousselin – Molecular Ecology Resources

Plant, root, and soil microbiome

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences – Shailendra Yadav – Archaea

Waste treatment microbiology

The Relationship between Microbial Community Evenness and Function in Slow Sand Filters – Sarah-Jane Haig – mBio

Metagenomics and bioinformatics

Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach – Shun’ichi Ishii – Scientific Reports

Exact approaches for scaffolding – Mathias Welle – BMC Bioinformatics

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities – Andreas Henschel – PLOS Computational Biology

Viruses and phages

A classification system for virophages and satellite viruses – Mart Krupovic – Virology Division News

Microbial Ecology

Research Highlight: Single-locus changes perturb community structure – Denise Waldron – Nature Review Genetics
Single gene locus changes perturb complex microbial communities as much as apex predator loss – Deirdre McClean – Nature Communications

Microbes in the news

New intro biology lab tests for germs on campus – Sydney Schaedel – The Daily Pennsylvanian

A Whale of a Tale: Gut microbiome of right whales and other baleen species shares characteristics with those of both cows and meat-eating predators – Bioscience Technology

Science and art

Artist Jennifer Angus Covers the Smithsonian’s Walls With Bugs – Lauren Palmer – ArtNet

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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 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 6, 2015

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General microbiome

Recurrent antibiotic exposure may promote cancer formation – Another step in understanding the role of the human microbiota? – Ben Boursi – European Journal of Cancer

Pregnancy and birth microbiome

Clinical chorioamnionitis at term VI: acute chorioamnionitis and funisitis according to the presence or absence of microorganisms and inflammation in the amniotic cavity – Roberto Romero – Journal of Perinatal Medicine

Pregnancy-related changes in the maternal gut microbiota are dependent upon the mother’s periconceptional diet – Wajiha Gohir – Gut Microbes

Potential NICU Environmental Influences on the Neonate’s Microbiome: A Systematic Review – Hartz, Lacey E. – Advances in Neonatal Care

Human oral microbiome

Analysis of the Microbiota of Black Stain in the Primary Dentition – Yue Li – PLOS ONE

Human gut microbiome

Furry pets modulate gut microbiota composition in infants at risk for allergic disease –
Merja Nermes – The Journal of Allergy and Clinical Immunology

Gut microbiome in Chronic Kidney Disease – Maria R. Wing – Experimental Physiology

Editorial: Microbial growth dynamics and human disease – Julia A. Segre – Science

Animal microbiome

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

454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils – Huxley M. Makonde – Springer Plus

Fish: Study of the microbiome of the intestine of the Comephorus dybowski korotneff, 1904 – N. L. Bel’kova – Ecology

Plant, root, and soil microbiome

An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota – T.H. Mauchline – Environmental Microbiology

Selection of biological indicators appropriate for European soil monitoring – D. Stone – Applied Soil Ecology

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere – Wouter Sillen – Soil Biology and Biochemistry

Arbuscular mycorrhiza symbiosis in viticulture: a review – Sophie Trouvelot – Agronomy for Sustainable Development

Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants – Michael Hemkemeyer – Soil Biology and Biochemistry

Differential responses of total and active soil microbial communities to long-term experimental N deposition – Zachary B. Freedman – Soil Biology and Biochemistry

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change

Built environment microbiome

Thesis: The building science of office surfaces: implications for microbial community succession – Mahnaz Zare – University of Toronto

Microbial Ecology

Dynamics of an experimental microbial invasion – Francisco Acosta – PNAS

Click to access 1505204112.full.pdf

Bioinformatics

metaModules identifies key functional subnetworks in microbiome-related disease – Ali May – Bioinformatics

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data – Jane Hawkey – BMC Genomics

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data – Gregory K. Farrant – BMC Bioinformatics

Inferring microbial interaction network from microbiome data using RMN algorithm
Kun-Nan Tsai – BMC Systems Biology
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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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August 12, 2015

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Drug metabolism by gut microbiota, nature vs. nurture in inbred strains of mice, gnotobiotic Drosophila, bat virome, and influence of protist predation on marine microbiomes.

General microbiome

Short-chain fatty acids in control of body weight and insulin sensitivity – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and birth microbiome

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci – Virginia Martín – Journal of Human Lactation

Human gut microbiome

Editorial: Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Hollie I Swanson – Drug Metabolism and Disposition
Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids – Curtis D. Klaassen – Drug Metabolism and Disposition

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing – Chika Kasai – BMC Gastroenterology

Animal and other models

Microbiota in 110 diverse inbred strains of mice: Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model – Kakolie Goswami – Infection and Immunity

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats – Kimberly A. Cox-York – Physiological Reports

Studying host-microbiota mutualism in Drosophila: Harnessing the power of gnotobiotic flies – Dali Ma – Biomedical Journal

MyD88 Signaling Regulates Steady-State Migration of Intestinal CD103+ Dendritic Cells Independently of TNF-α and the Gut Microbiota – Karin Hägerbrand – The Journal of Immunology

Animal microbiome

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases – Zhiqiang Wu – ISME Journal

Plant, root, and soil microbiome

Host promiscuity in symbiont associations can influence exotic legume establishment and colonization of novel ranges – Metha M. Klock – Diversity and Distributions

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Water microbiome

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions – Federico Baltar – ISME Journal

Waste and water treatment microbiology

The activated sludge ecosystem contains a core community of abundant organisms – Aaron M Saunders – ISME Journal

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system – Fangqiong Ling – ISME Journal

More microbes

Levels and limits in artificial selection of communities – Manuel Blouin – Ecology Letters

Editorial: Origin of the Yeast Whole-Genome Duplication – Kenneth H. Wolfe – PLOS Biology
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage – Marina Marcet-Houben – PLOS Biology

Microbes in the news

Global Human Microbiome Market: Asia is expected to show high growth rates by 2020 – MedGadget

Things I Tell My Mom: Five ways for you to participate in science – Cathy Seiler – Ahwatukee Foothills News

Why making and taking fermented drinks is becoming popular again – John McKenna – The Irish Times

Protein Goes Green: Can Algae Become The Next Soy? – Jessie Rack – NPR

Cultured Coffee offers the flavor of poop-brewed coffee without the crap – TJ Dietsch – Geek

Making kefir at home is easy, healthy – Kit Waskom Pollard – Baltimore Sun

‘Genomic Archaeology’ Reveals That Lager Yeast Was Born More Than Once – Andrea Alfano -Tech Times

Researchers resurrect extinct virus to use for gene therapy: Evolutionary ancestors remade based on current viruses – Ars Technica

Science, publishing, and career

Make Peer Review Public: How to make science faster and more robust – Adam Marcus and Ivan Oransky – Slate

Despite concerted effort, barriers to women in science remain – Jennifer Ann Thomson – The Conversation

Outreach: Primary School outreach – inspiring young minds with science – Mariya Lobanovska – SGM

Physics: She did it all: Val Gibson enjoys the autobiography of Mary K. Gaillard, the first female physics professor at Berkeley – Val Gibson – Nature

Bik’s Picks

Octopus Genome Offers Insights Into One Of Ocean’s Cleverest Oddballs – Nell Greenfieldboyce – NPR

Meteor time! How to watch the big Perseid shower – Paul Rogers – San Jose Mercury News

MIT tackling more serious science: they program beer-delivering robots – ZME Science

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August 5, 2015

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Microbiome in patients with Irritable Bowel Syndrome, gastric bypass operations induces long-term microbiome changes, environmental enteropathy in a mouse model, respiratory viruses in large families, and microbiology of restaurant grease waste.

Events

Microbiome R&D and Business Collaboration Forum – September 10-11, 2015, San Diego, USA

European Microbiome Congress 2015 – 18 and 19 November 2015, London, UK

Microbiome of pregnancy and birth

Review: Antibiotics and the developing infant gut microbiota and resistome – Molly K Gibson – Current Opinion in Microbiology

Review: Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System – Cong, Xiaomei – Advances in Neonatal Care

Review: The Prescient Placenta – Christopher Coe – The Scientist

Human respiratory microbiome

Community Surveillance of Respiratory Viruses Among Families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) Study –  L. Byington – Clinical Infectious Diseases

Human gut microbiome

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome – Marta Pozuelo – Scientific Reports

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation – Valentina Tremaroli – Cell Metabolism

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline – Clara Barrios – PLOS ONE

Editorial: Microbiome reflects status of RA and response to therapy – Robert Phillips – Nature Reviews Rheumatology

Microbiome models

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus – Kristian Daly – Environmental Microbiology

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model – Eric M. Brown – Nature Communications

Animal microbiome

Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose – Masahiro Yuki – Environmental Microbiology

Two gut community enterotypes recur in diverse bumblebee species – Jilian Li- Current Biology

Unique metabolites protect earthworms against plant polyphenols – Manuel Liebeke – Nature Communications

Streptococcus panodentis sp. nov., from the oral cavities of chimpanzees – Masaaki Okamoto – Microbiology and Immunology

Plant, root, and soil microbiome

Fungal root endophytes of Quercus robur subjected to flooding – H. Kwaśna – Forest Pathology

Land Use and Precipitation Affect Organic and Microbial Carbon Stocks and the Specific Metabolic Quotient in Soils of Eleven Ecosystems of Mt. Kilimanjaro, Tanzania – Holger Pabst – Land Degradation & Development

The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA – Laura Lee Sims – Mycologia

Bacterial community structures as a diagnostic tool for watershed quality assessment – Luigimaria Borruso – Research in Microbiology

Water microbiome

Planktonic and sedimentary bacterial diversity of Lake Sayram in summer – Lei Fang – Microbiology Open

Waste and bioreactor microbiome

Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages – Vahid Razaviarani – Bioresource Technology

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Metagenomics and bioinformatics

Xander: employing a novel method for efficient gene-targeted metagenomic assembly – Qiong Wang – Microbiome

Metabolomics

Symposium report: Olfaction in the Kidney: ‘Smelling’ gut microbial metabolites – Niranjana Natarajan and Jennifer L. Pluznick – Experimental Physiology

Microbial Ecology

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment – Hasan Celiker & Jeff Gore – Nature Communications

Microbes in the news

Interview with Peter DiLaura, CEO of Second Genome: Data Mining The Microbiome Toward A Cure For Inflammatory Disease – Peter High – Forbes

Weight loss surgery benefits for gut microbiome last at least a decade – MedicalXpress

Extreme weight loss surgery works, but is it thanks to the knife—or the microbes? – Mitch Leslie – Science

A Belated Look at New York’s Cooling Towers, Prime Suspect in Legionnaires’ Outbreak – Winnie Hu and Noah Remnick – NY Times

Amid Legionnaires’ Fears, City Proposes New Cooling Tower Rules – Mara Gay and Corinne Ramey – Wall Street Journal
Randomised clinical study: Aspergillus niger-derived enzyme digests gluten in the stomach of healthy volunteers – B. N. Salden – Alimentary Pharmacology & Therapeutics

Study: Citrus Greening Bacterium Gives Vector Unexpected Boost – Paul Rusnak – Growing Produce

Team identifies mutations that allow bacteria to resist antibiotics – Phys.org

Africa is within reach of being declared a polio free region – The Conversation

Viruses Thrive In Big Families, In Sickness and In Health – University of Utah

Science, career, and publishing

Where Next for Genetics and Genomics? – Chris Tyler-Smith – PLOS Biology

Tech Women Triumph: $30k Funding In A Day, Success Under Pressure, True Leaders Inspire – Leo King – Forbes

#ilooklikeanengineer wants to challenge your ideas about who can be a scientist – Susan Svrluga – Washington Post

#FieldWorkFail: Gluing Yourself to a Live Crocodile and Other Mistakes: Scientists share the gross, scary, and often hilarious reality of doing experiments in the wild – Robinson Meyer – The Atlantic

9 Scientists Told Us What Scares Them The Most – Kelly Oakes – BuzzFeed

Bik’s Picks

Jack the Ripper’s final victim set to be exhumed following new theory on the killer’s identity – Doug Bolton – Independent

Scientists unearth earthworm’s ability to digest plant toxins – LiveMint

Are monarch butterflies really being massacred? A new study says it’s a lot more complicated than it seems – Sarah Kaplan – Washington Post

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