Category Archives: Food Microbiology

March 6, 2015

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Pregnancy and birth

Longitudinal Analysis of the Premature Infant Intestinal Microbiome Prior to Necrotizing Enterocolitis: A Case-Control Study – Yanjiao Zhou – PLOS ONE

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota – Tadao Enomoto – Allergology International

Human oral microbiome

Subgingival Microbial Communities in Leukocyte Adhesion Deficiency and Their Relationship with Local Immunopathology – Niki M. Moutsopoulos – PLOS Pathogens

Human gut microbiome

What is missing from this title? 16S gut community of the Cameron County Hispanic Cohort – Matthew C Ross – Microbiome

Review: The role of intestinal microbiota in acute graft-versus-host disease – Yuanyuan Chen – Journal of Immunology Research

Review: Type 1 diabetes and gut microbiota: Friend or foe? – Changyun Hu – Pharmacological Research

Review: Collective unconscious: how gut microbes shape human behavior
Timothy G. Dinan- Journal of Psychiatric Research

Human respiratory microbiome

2013 Workshop summary: Host–microbe interactions in distal airways: relevance to chronic airway diseases – Clémence Martin – European Respiratory Review

Review: Microbial Exposure and Onset of Allergic Diseases – Potential Prevention Strategies? – Petra Ina Pfefferle, Harald Renz – Allergology International

Animal models of microbiome research

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome – Jun Wang – Nature Communications

Disturbance of the intestinal microbial community by ursolic acid contributes to its function as a regulator of fat deposition – Zemeng Feng – Journal of Functional Foods

Helicobacter hepaticus infection in BALB/c mice abolishes subunit-vaccine-induced protection against M. tuberculosis – Isabelle C. Arnold – Vaccine

Animal microbiome

Early life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

In cattle: Characterization of mucosa-associated bacterial communities in abomasal ulcers by pyrosequencing – Alexandra Hund- Veterinary Microbiology

Baby marmosets (Do a Google Image search)! Isolation and identification of cultivable Bifidobacterium spp. from the faeces of 5 baby common marmosets (Callithrix jacchus L.) – Samanta Michelini – Anaerobe

A Kazal-type inhibitor is modulated by Trypanosoma cruzi to control microbiota inside the anterior midgut of Rhodnius prolixus – Tatiane S. Soares – Biochimie

Plant microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Soil and sediment microbiome

A Method for Determining Community Level Physiological Profiles of Organic Soil Horizons – Mathew J.B. Swallow and Sylvie A. Quideau – Soil Science Society of America Journal

Influence of elevated ozone concentration on methanotrophic bacterial communities in soil under field condition – Y.Z. Huang – Atmospheric Environment

Disruption of photoautotrophic intertidal mats by filamentous fungi – Cátia Carreira – Environmental Microbiology

Phylogenetically distinct phylotypes modulate nitrification in a paddy soil – Jun Zhao – Applied and Environmental Microbiology

Water microbiome

Metagenomic analysis of a high CO2 subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla – Joanne B. Emerson – Environmental Microbiology

Effect of historical residual hexachlorocyclohexanes and dichlorodiphenyltrichloroethane on bacterial communities in sediment core collected from an estuary in northeastern China by next-generation sequencing – Jianguo Guo – Marine Pollution Bulletin

Understanding diversity patterns in bacterioplankton communities from a Sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria (“Candidatus Thiopilula spp.”) from abyssal cold seeps of the Barbados Accretionary Prism – Daniel S. Jones – Applied and Environmental Microbiology

Bioreactor microbiome

Long-term dynamics of the microbial community in a full-scale wastewater treatment plant – A. Muszyński – International Biodeterioration & Biodegradation

Microbiome of the built environment

Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities – Tamar Dickerson – Online Journal of Public Health Informatics

Food microbiology

Yeast strains as potential aroma enhancers in dry fermented sausages – Mónica Flores – International Journal of Food Microbiology

Metagenomics and bioinformatics

IVA: accurate de novo assembly of RNA virus genomes – Martin Hunt – Bioinformatics

Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels – Rika A. Furuta – Transfusion

Review: Fungal genome sequencing: basic biology to biotechnology – Krishna Kant Sharma – Critical Reviews in Biotechnology

Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis – Qizhi Cao – Gut

Proteomics

Review: Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Microbial Ecology

Predicting ecosystem emergent properties at multiple scales – Jack A. Gilbert and Chris Henry – Environmental Microbiology Reports

Perspective: Re-defining microbial diversity from its single-celled building blocks – Ramunas Stepanauskas – Environmental Microbiology Reports

Microbes in the news

Not Even Science Could Explain the Bacteria In My Apartment – Sarah Zhang – Gizmodo

Gut microbial mix relates to stages of blood sugar control – Medical Xpress
Gut bacteria may contribute to diabetes in black males – Sharon Parmet – University of Illinois at Chicago

Who owns my microbiome? – Gabrielle Morguelan – Transylvania Rambler

Bill Gates Foundation backs microbiome engineering to boost infant health – Shane Starling – Nutraingredients

Antarctic lakes are full of small surprises – Sarah Payne – Australian Antarctic Magazine

Long list of food items in alphabetical order, but not much science: The human microbiome: How to feed your gut – Mindy Athas – Baltimore Sun

Science, publishing, and career

Need registration to read: It starts with a poster: Most researchers learn how to talk about science at meetings – Marcia McNutt – Science

Why has the scholarly journal endured? – Alice Meadows – Exchanges at Wiley

Reflecting on Fifty Years of Progress for Women in Science – Nancy Hopkins – DNA and Cell Biology

Bik’s Picks

Video: Giant Octopus makes slippery escape from tank in Seattle aquarium – Ben Axelson – Syracuse

CCTV unexpectedly catches rare wild giant panda on midnight stroll – Rose Troup Buchanan – Independent

Turning yogurt waste into new products – University of Wisconsin-Madison – Science Daily

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March 3, 2015

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Human microbiome general

Manuscript: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes and Other Selfish Entities Shape Our Behavior – Peter Kramer and Paola Bressan

Microbiome of pregnancy and birth

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development – Tali Raveh-Sadka – eLIFE

Human respiratory microbiome

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals – Christine M. Bassis – mBio

Human gut microbiome

The relevance of intestinal dysbiosis in liver transplant candidates – M. Grąt – Transplant Infectious Disease

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohn’s Disease – Suskind, David L. – Inflammatory Bowel Diseases

Review: The Guts of Obesity: Progress and Challenges in Linking Gut Microbes to Obesity  – Gabriel A. Al-Ghalith – Discovery Medicine

Animal models of microbiome research

Thesis: Exercise is more effective at producing robust, lasting changes in gut microbial composition in juvenile than in adult male F344 rats – Agnieszka Mika – University of Colorado at Boulder

The gut microbiome restores intrinsic and extrinsic nerve function in germ-free mice accompanied by changes in calbindin – K. A. McVey Neufeld – Neurogastroenterology & Motility

Cystic fibrosis mouse model-dependent intestinal structure and gut microbiome – Mark Bazett – Mammalian Genome

Use of bacteriocin-producing, probiotic strain Enterococcus faecium AL41 to control intestinal microbiota in farm ostriches – Andrea Lauková – Letters in Applied Microbiology

Animal microbiome

Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses – Shaufi M Mohd Asrore – Gut Pathogens

Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens – Douglas C. Woodhams – Ecological Archives

Diet shapes the gut microbiota of the omnivorous cockroach Blatella germanica – Ana Elena Pérez-Cobas – FEMS Microbiology Ecology

Characterization of the honey bee microbiome throughout the queen-rearing process – David R. Tarpy – Applied and Environmental Microbiology

Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand-islands reef complex, West-Java, Indonesia – Nicole J. de Voogd – FEMS Microbiology Ecology

Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf – B. C. C. Hume – Scientific Reports

Plant microbiome

Grazing livestock are exposed to terrestrial cyanobacteria – Bruce C McGorum – Veterinary Research

Soil and root microbiome

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere –
Chanyarat Paungfoo-Lonhienne – Scientific Reports

Changes in soil microbial community structure and activity in a cedar plantation invaded by moso bamboo – Ed-Haun Chang, Chih-Yu Chiu – Applied Soil Ecology

Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities – Kristin Aleklett – PeerJ

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site – Indumathy Jayamani, Alison M. Cupples – Environmental Science and Pollution Research

Impact of metal pollution on fungal diversity and community structures – Michiel Op De Beeck – Environmental Microbiology

Water microbiome

Diverse uncultivated ultra-small bacterial cells in groundwater – Birgit Luef – Nature Communications

Impacts of the Three Gorges Dam on microbial structure and potential function – Qingyun Yan – Scientific Reports

Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean – Rosemary E. Scavotto – Environmental Microbiology

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India) – Sheryl Oliveira Fernandes – Brazilian Journal of Microbiology

Bioreactor microbiology

Start-up strategies in manure-fed biogas reactors: Process parameters and methanogenic communities – M. Goberna – Biomass and Bioenergy

Microbiome of the built environment

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China – Huirong Lin – BioMed Research International

Observational scores of dampness and mold associated with measurements of microbial agents and moisture in three public schools – S. J. Cho – Indoor Air

Food microbiology

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome – Armin Erlacher – PLOS ONE

Phages and viruses

‘Ménage à trois’: a selfish genetic element uses a virus to propagate within Thermotogales – Julien Lossouarn – Environmental Microbiology

Microbial Ecology

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession – Francisco Dini-Andreote – PNAS USA

The community ecology of pathogens: coinfection, coexistence and community composition – Eric W. Seabloom – Ecology Letters

Tuberculosis: Fighting an old disease with next-generation sequencing – Anzaan Dippenaar, Robin M. Warren – eLIFE

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen – Braham Dhillon – PNAS USA

A tortoise-infecting picornavirus expands the host range of the family Picornaviridae
Terry Fei Fan Ng – Archives of Virology

Metagenomics and bioinformatics

Review: Insights from 20 years of bacterial genome sequencing – Miriam Land – Functional & Integrative Genomics

Review: The Current Status and Challenges in Computational Analysis of Genomic Big Data – Yiming Qin – Big Data Research

Metabolomics

Impact of storage conditions on metabolite profiles of sputum samples from persons with cystic fibrosis – Jiangchao Zhao – Journal of Cystic Fibrosis

Microbes in the news

Enter the Vaginome: Meet the Microbes that Live in Our Vaginas – A.V. Flox – Motherboard

New paper on diseased vs healthy infants in a NICU, possible impacts for future hospital microbiome work – Bubba Brooks – MicroBEnet

Archaea: Mysterious microbes hold big possibilities for Sloan Research Fellow Alyson Santoro – EurekaAlert

Genes & cells: Jet lag disrupts microbes in the gut: Mice with time-shifted bacteria develop metabolic problems – Tina Hesman Saey – Science News

The environment may change, but the microbiome of queen bees does not – Matt Shipman

Cheesey Microbial Communities – Daniel P. Haeusser – Small Things Considered

150,000 of these bacteria could fit on the tip of a hair (and that’s about as small as life can get) – Rachel Feltman – Washington Post

Unusual Bacteria Discovered In Deepest Ocean Trench – Ocean Leadership

Link Identified Between Virus Recognition, Destruction in Bacterial Immune System – Infection Control Today
Researchers Discover How Bacteria ‘Steal’ Genetic Information – Jim Algar – Tech Times

Science, publishing, and career

Different personal propensities among scientists relate to deeper vs. broader knowledge contributions – Thomas S. Bateman, and Andrew M. Hess – PNAS USA
Attention, All Scientists: Do Improv, With Alan Alda’s Help – Kenneth Chang – New York Times

Bik’s Picks

Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa –
Fabrice Lihoreau – Nature Communications

Termites: Guardians of the Soil – Natalie Angier – New York Times

A social chemosignaling function for human handshaking – Idan Frumin – eLIFE

Snip, Snap, Slurp: Misophonia Makes Them Unbearable – What sound most grates on your nerves? – Karen Barrow – New York Times
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March 2, 2015

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General microbiome papers

Review: The Microbiome: A Contributor to Health and Disease – Bailus Walker Jr. – Journal of the Health Care for the Poor and Underserved

Human oral microbiome

Transduction-mediated horizontal gene transfer in the oral microbiome – Roy H. Stevens – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Review: The lung mycobiome: an emerging field of the human respiratory microbiome – Linh D. N. Nguyen – Frontiers in Microbiology

Human gut microbiome

Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages – Se-Hoon Park – BMC Microbiology

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality – Yanfei Chen – Journal of Gastroenterology and Hepatology

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj – Abiola Olumuyiwa Olaitan – International Journal of Antimicrobial Agents

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Human vaginal microbiome

Correlates of the molecular vaginal microbiota composition of African women – Raju Gautam – BMC Infectious Diseases

Animal microbiome

In chickens: Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences – Dragana Stanley – BMC Microbiology

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh – Andrea M. Larsen – Microbial Ecology

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences – Sandra Pucciarelli – Microbial Ecology

Plant microbiome

Phenotypic and genetic characterization of rhizobia isolated from Hedysarum flexuosum in Northwest region of Morocco – Fatima Ezzakkioui – Journal of Basic Microbiology

Biotic and abiotic predictors of fungal colonization in grasses of the Colorado Rockies – Luciana B. Ranelli – Diversity and Distributions

Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Martina Köberl – Frontiers in Microbiology

Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. – Armin Erlacher – Frontiers in Microbiology

Soil and sediment microbiome

Agricultural intensification and the functional capacity of soil microbes on smallholder African farms – Stephen A. Wood – Journal of Applied Ecology

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees – Michaela Urbanová – Soil Biology and Biochemistry

Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia – Robert Duran – Environmental Science and Pollution Research

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation – Maria E. Hernandez – PeerJ

Water microbiome

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs – Peter Menzel – Microbial Ecology

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients – Jiwen Liu – Frontiers in Microbiology

Microbiome of the built environment

Thesis: Longitudinal and spatial characterization of microbial communities in offices – John Chase – Northern Arizona University

Bacterial transfer to beverages during drinking games: ‘beer pong’ – Paul L. Dawson – Int. J. Food Safety, Nutrition and Public Health

Food microbiology

High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia – Wenjun Liu – BMC Microbiology

Microbiological Changes and Biodiversity of Cultivable Indigenous Bacteria in Sanbao Larger Yellow Croaker (Pseudosciaena crocea), a Chinese Salted and Fermented Seafood – He Zhang – Journal of Food Sciences

Bioreactor microbiology

A methodological framework for linking bioreactor function to microbial communities and environmental conditions – Francis L de los Reyes III – Current Opinion in Biotechnology

Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing – Haihan Zhang – BMC Microbiology

Phages and viruses

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales – Uri Gophna – ISME Journal

Inactivation of an Enveloped Surrogate Virus in Human Sewage – Lisa M. Casanova – Environ. Sci. Technol. Lett.

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing – Friederike S. Rossmann – PLOS Pathogens

Archaea

Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing – Vanessa D. Nkamga – Current Microbiology

Bioinformatics and metagenomics

The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: Case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia – E. González-Tortuero – Molecular Ecology Resources

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics – Sandeep K Kushwaha – BMC Bioinformatics

Spaced seeds improve metagenomic classification – Karel Bˇrinda – ArXiv

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K – Naama M. Kopelman – Molecular Ecology Resources

PhD thesis: Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome – Sharon I. Greenblum – University of Washington

Masters thesis: MR-CUDASW – GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data – Amir Muhammadzadeh

Testing ecological theories with sequence similarity networks: marine ciliates
exhibit similar geographic dispersal patterns as multicellular organisms – Dominik Forster – BMC Biology

A Brief Review of Software Tools for Pangenomics – Jingfa Xiao – Genomics, Proteomics & Bioinformatics

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes – Xavier Didelot – PLOS Computational Biology

Ten years of pan-genome analyses – George Vernikos – Current Opinion in Microbiology

Metabolomics and proteomics

Towards further defining the proteome of mouse saliva – Anne A Blanchard – Proteome Science

Protein Complexes in Bacteria – J. Harry Caufield – PLOS Computational Biology

Review: Metabolomics and Diabetes: Analytical and Computational Approaches – Kelli M. Sas – Diabetes

Techniques

Inosine at Different Primer Positions to Study Structure and Diversity of Prokaryotic Populations – Eitan Ben-Dov and Ariel Kushmaro – Current Issues Molecular Biology

Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil – Hannes Schmidt – Soil Biology and Biochemistry

Microbes in the news

Diet, Location And Your Kid’s Gut Bacteria – Stefania Hartley – Asian Scientist Magazine

Killing off one Bacterium Can Lead to Obesity – Noel Angeles – SMN Weekly

The Human Microbiome Through an Oral Healthcare Lens – Natasha Singh – Oral Health Group

Yes Virginia, there is a paper on microbial transfer during beer pong – Jonathan Eisen

First detailed evidence of bacteria at the lower size limit of life – Science Codex

How Small Can Life Get? These Ultra-Small Bacteria May Be At The Limit – Science 2.0

Title Fail: Deadly bacteria outbreak linked to UCLA microscopes – Standard Examiner

The bioMASON Startup Grows Bricks from Bacteria – Annie Pilon – Small Biz Trends

Deadly bacteria release sparks concern at Louisiana lab – Alison Young – USA Today

Science, publishing and career

Riding Out Rejection: How to navigate the choppy waters of scientific publication – Kate Yandell – The Scientist

Medical Journals and Free Speech – Joel Bakan – Pediatrics

How to Write a Presubmission Inquiry – Thomas Lengauer, Ruth Nussinov – PLOS Computational Biology

Chill GPS: Keeping track of frozen biological samples – Jeffrey M. Perkel – The Scientist

Science and Art

Move over #TheDress and #LlamaDrama, this weekend’s Twitter storm was all about #SciArt – Twitter

Bik’s Picks

Scientists have created the perfect music for cats – Fiona MacDonald – Science Alert

Gulf of Mexico Turns Deadly for Dolphins – Rachel Nuwer – New York Times

‘Skeletorus’ and ‘Sparklemuffin’ the Newest Spiders – Agata Blaszczak Boxe – Live Science

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February 13, 2015

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Happy Valentine’s Day tomorrow! The totally awesome Michele Banks @artologica made a super-special #ScienceValentines for all microbiome lovers.

Microbiome of pregnancy and birth

Review (but plagiarism alert!): Gut microbiota biomodulators: When the stork comes by the scalpel – Vito Leonardo Miniello – Clinica Chimica Acta

Human oral microbiome

Preliminary Report of the Effect of A New Saliva Substitute Based on Chamomile (Matricaria Chamomilla) and Flax Seed (Linum Usitatissimum) on the Oral Microbiota of Patients with Xerostomia – Blanca Urzúa Orellana – Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

Human vaginal microbiome

Also check out “Animal microbiome” section below.

Review: The biology of Trichomonas vaginalis in the light of urogenital tract infection – Gary Kusdian, Sven B. Gould – Molecular and Biochemical Parasitology

Human gut microbiome

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell

Review: Impact of diet on the human intestinal microbiota – Huizi Tan, Paul W. O’Toole – Current Opinion in Food Science

Fecal Microbiota Transplantation

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Krishna Rao – Infectious Disease Clinics of North America

Survey: Faecal Microbiota Transplantation for Clostridium difficile infection in the UK – Robert James Porter, Carole Fogg – Clinical Microbiology and Infection

Animal models

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract – Mark J. Koenigsknecht – Infection and Immunity

Animal microbiome

Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis) – M. Uchihashi – American Journal of Primatology

Genetically Modifying the Insect Gut Microbiota to Control Chagas Disease Vectors through Systemic RNAi – Mabel L. Taracena – PLOS Neglected Tropical Diseases

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix – Olga Pantos – ISME Journal

Soil microbiology

Review: Microbial hotspots and hot moments in soil: Concept & review – Yakov Kuzyakov, Evgenia Blagodatskaya – Soil Biology and Biochemistry

Water microbiology

Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek’s watershed – A.L. Barkovskii – Journal of Applied Microbiology

Food microbiology

Microbial biogeography of the transnational fermented milk Matsoni – Nicholas A. Bokulich – Food Microbiology

The microbial diversity of an industrially produced lambic beer shares members of a traditionally produced one and reveals a core microbiota for lambic beer fermentation – Freek Spitaels – Food Microbiology

Bacteria and yeast microbiota in milk kefir grains from different Italian regions – Cristiana Garofalo – Food Microbiology

Review: Phages in the global fruit and vegetable industry – M. Żaczek – Journal of Applied Microbiology

Metabolomics

Review: The human gut sterolbiome: bile acid-microbiome endocrine aspects and therapeutics – Jason M. Ridlon, Jasmohan S. Bajaj – Acta Pharmaceutica Sinica B

Bioinformatics

Reconstructing (super)trees from data sets with missing distances: Not all is lost – George Kettleborough – Molecular Biology and Evolution

Microbial evolution

Harnessing Evolution to Elucidate the Consequences of Symbiosis – Nicole M. Gerardo – PLOS Biology

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands – Florent Lassalle – PLOS Genetics

Microbes in the news

Nicely timed: Romance and Microbes: The Science Behind Shared Bacteria – Brittany Dingler – Skidmore News

Negative Effects of Long-Term Antibiotic Use Even Far-More Reaching Than Estimated – Heather Johnson – Business2Community

Antibiotic use has more unwanted effects than previously thought – Catharine Paddock – Medical News Today

Not gross if you love microbes: 5 Gross Things Inside Your Body Right Now! (video) – Scientiflix

The 3 strangest facts about all that bacteria on the New York City subway – Erin Brodwin – BusinessInsider

What do the bacteria living in your gut have to do with your immune system? – Elizabeth Bent – The Conversation

Pensioner Peter cured by groundbreaking transplant – West Briton

Since 1938: Autism, The Microbiome and Donald Triplett, Case 1 – Teresa Conrick – The Age of Autism

Captive pandas succumb to killer virus – Mara Hvistendahl – Science

Does the Cold Really Cause a Cold? – James Gilbert – NewsPlex

Study: Listeria pathogen is prevalent, persistent in retail delis – Purdue University

Toxic Ganges adds to spread of drug-resistant bacteria – Victor Mallet and Clive Cookson – FT

Science, publishing, and career

Slideshow: So you want to be an academic? – Josh Neufeld – SlideShare

The science of schmoozing – about scientist Hugues Lantuit – Eli Kintisch – Science

Inspiring Women Scientists in Microbiology and Ecology (part 1) – Suzanne Kennedy – MoBio

Inspiring Women Scientists in Microbiology and Ecology: Part Deux – Emelia DeForce – MoBio

Why Did WNYC Delete Its Podcast on the Male “Expert” on Women in Tech? – Kate Knibbs – Gizmodo

Bik’s Picks – Valentine’s day’s edition

The Chemical Compounds Behind the Smell of Flowers – Compound Chemistry

This Valentine’s Day, Say ‘I Love You’ With Science – Brandon Echter – Science Friday

7 DIY valentine ideas for science nerds – Jenn Savedge – Mother Nature Network

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February 9, 2015

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Human oral microbiome

Pulp and plaque microbiotas of children with severe early childhood caries – Natalia I. Chalmers – Journal of Oral Microbiology

Analysis of oral microbial community and Th17-associated cytokines in saliva of patients with oral lichen planus – Kun Wang – Microbiology and Immunology

Human gut microbiome

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities – Jiachao Zhang – The ISME Journal

Distinct gut microbiota of healthy children from two different geographic regions of Thailand – Orawan La-ongkham – Archives of Microbiology

An Appropriate Cutoff Value for Determining the Colonization of Helicobacter pylori by the Pyrosequencing Method: Comparison with Conventional Methods – Jaeyeon Kim – Helicobacter

Review: Dysbiosis of the gut microbiota in disease – Simon Carding – Microbial Ecology in Health and Disease

Review: Manipulating the gut microbiota to maintain health and treat disease – Karen P. Scott – Microbial Ecology in Health and Disease

Fecal Transplants

Successful treatment of severe sepsis and diarrhea after vagotomy utilizing fecal microbiota transplantation: a case report – Qiurong Li – Critical Care

Animal models of microbiome research

Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs – Marcio C Costa – BMC Veterinary Research

Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract – Jyoti Shankar – Scientific Reports

Gut microbial markers are associated with diabetes onset, regulatory imbalance, and IFN-γ level in NOD Mice – Ł. Krych – Gut Microbes

Defective NOD2 peptidoglycan sensing promotes diet-induced inflammation, dysbiosis, and insulin resistance – Emmanuel Denou – EMBO Journal

Animal Microbiome

Internal Extracellular Bacteria of Diaphorina citri Kuwayama (Hemiptera: Psyllidae), the Asian Citrus Psyllid – Lakshmi D. Kolora – Current Microbiology

Soil Microbiome

Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem – Jun-Tao Wang- Journal of Soils and Sediments

Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics – Dini Nurdiani – Journal of Bioscience and Bioengineering

Microbial diversity of mangrove sediment in Shenzhen Bay and gene cloning, characterization of an isolated phytase-producing strain of SPC09 B. cereus – Shengpeng Zhang – Applied Microbiology and Biotechnology

Food Microbiology

Zooming into food-associated microbial consortia: A “cultural” evolution
Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Review: Emerging DNA-based technologies to characterize food ecosystems – Andrea Galimberti – Food Research International

Bioreactor microbiology

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities – Wuttichai Mhuantong – Biotechnology for Biofuels

Metabolomics

Defining the Microbial Effluxome in the content of the Host-Microbiome Interaction – Anastasios Ioannidis – Frontiers in Pharmacology

Reference-free comparison of microbial communities via de Bruijn graphs – Serghei Mangul and David Koslicki – preprint

A systematic evaluation of high-dimensional, ensemble-based regression for
exploring large model spaces in microbiome analyses – Jyoti Shankar – BMC Bioinformatics

Microbial Ecology

Opinion: Landscape community genomics: understanding eco-evolutionary processes in complex environments – Brian K. Hand – Trends in Ecology & Evolution

Techniques

Accurate, multi-kb reads resolve complex populations and detect rare
microorganisms – Itai Sharon – Genome Research

A simple separation method for downstream biochemical analysis of aquatic microbes – Cody E. Garrison, Alexander B. Bochdansky – Journal of Microbiological Methods

Microbes in the News

How to Make Breakfast With Your Vagina – Janet Jay – Motherboard

Breast IS best: Researchers say babies get microbes from mother’s milk that makes them ‘more ready’ to digest solid food – Mark Prigg – Daily Mail

Common antibiotics trigger significant changes in equine gut bacteria – study – Horsetalk

The Hungry Microbiome Part 4: The colon, colon cancer, and butyrate – Jesse Hawley – CSIRO

Google Maps for bacteria? How NYC subway swab could change public health (Podcast) – PBS Newshour

Investigation into possible spread of bacteria found in local primate center – Ashley Rodrigue – WWLTV

What friendly bacteria really CAN do for you… but probiotic makers are banned from telling us about – Sadie Nicholas – DailyMail UK

Bacteria Hysteria: ‘Bacteria and mold will accumulate’: Expert weighs in on bath towel use – Fox8.com

Gut Bacteria Differs in Gluten-free Celiac Patients with Persistent Symptoms – Jefferson Adams – Celiac.com

Bacterial DNA from the Black Death found in teeth – Yngve Vogt – MedicalXpress

UC Merced graduate student to continue oral bacteria research in Brazil – Ana B. Ibarra – Mercedsunstar

Meet the Poop-Sniffing Dogs That Are Saving Endangered Wildlife – Charyn Pfeuffer – Wired

Experimental drug containing tiny fragments of teenage acne bacteria trialled on MS patients – Lucie van den Berg – Herald Sun

Bacteria’s hidden traffic control – Phys.org

Science, publishing, career

How not to write a sequence assembly comparison paper – Keith Robison – Omics!Omics!

Research Misconduct Identified by the US Food and Drug Administration
Out of Sight, Out of Mind, Out of the Peer-Reviewed Literature – Charles Seiffe – JAMA Internal Medicine

Are Your Medications Safe? The FDA buries evidence of fraud in medical trials. My students and I dug it up. – Charles Seife – Slate

Bik’s Picks

The Champion Egg-Layers of the Bird World – Emma Bryce – Audubon

Enzyme rapidly reduces sulfites in wine – Tim Sandle – Digital Journal

NASA Mars Curiosity Rover Collects Soil Samples – Deborah Grace – Pierce Pioneer

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February 5, 2015

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Microbiome of pregnancy and birth

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes – Aleksandar D. Kostic – Cell Host & Microbe

Meeting abstracts in the Journal of Allergy and Clinical Immunology:
Influence of Infant Gut Microbiome on Development of Infant Regulatory T Cells – Kevin Bobbitt
The Infant Gut Microbiome Mediates the Association Between Breastfeeding and Allergic-like Response to Pets in Children – Alexandra R. Sitarik
Association of the Infant Gastrointestinal Microbiome with Nocturnal Symptoms in Children with Asthma – Albert M. Levin
Decrease in Diversity of Nasal Microbiota during Wheezing Episodes in Preschool Children – Gorka Alkorta-Aranburu

Maternal influences on fetal microbial colonization and immune development – Joann Romano-Keeler & Jörn-Hendrik Weitkamp – Pediatric Research

Human oral microbiome

Evaluation of human and microbial DNA content in subgingival plaque samples collected by paper points or curette – P.J. Pérez-Chaparro – Journal of Microbiological Methods

Human vaginal microbiome

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR – Takashi Kurakawa – Journal of Microbiological Methods

Human gut microbiome

Weight Gain After Fecal Microbiota Transplantation – Neha Alang and Colleen R. Kelly – Open Forum Infectious Diseases

The Gut Microbiota, Intestinal Permeability, Bacterial Translocation, and Nonalcoholic Fatty Liver Disease: What Comes First? – Erin Spengler, Rohit loomba – CMGH Cellular and Molecular Gastroenterology and Hepatology

$70 to read this one: Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy – Xiaobo Feng – The American Surgeon

Review: Gut Microbiota: Association with NAFLD and Metabolic Disturbances – E. Lau – BioMed Research International

Review: Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry – Eva M Selhub – Journal of Physiological Anthropology

Animal models of microbiome research

Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec – R. Khiaosa-ard – Journal of Dairy Science

Effect of feeding Jerusalem artichoke (Helianthus tuberosus) root as prebiotic on nutrient utilization, fecal characteristics and serum metabolite profile of captive Indian leopard (Panthera pardus fusca) fed a meat-on-bone diet – S.K. Pradhan – Zoo Biology

Comparative Analysis of Gastrointestinal Microbiota Between Normal and Caudal-Related Homeobox 2 (Cdx2) Transgenic Mice – Hirotsugu Sakamoto – Intestinal Research

Plant microbiome

Impact of mycorrhizal inoculation on the development of Intsia bijuga grown on soil under exotic species Casuarina equisetifolia plantation – Dina Ratahiriarisoa – Journal of Plant Sciences

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient – Susan G. Jarvis – New Phytologist

Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii – David H. Green – BioMed Research International

Review: The importance of the microbiome of the plant holobiont – Philippe Vandenkoornhuyse – New Phytologist

Soil microbiome

Soil microbial response to waste potassium silicate drilling fluid – Linjun Yao – Journal of Environmental Sciences

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218O – Elizabeth A. Rettedal and Volker S. Brözel – MicrobiologyOpen

Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils – Shamsa Akbar – Journal of Basic Microbiology

Microbiome of the built environment
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics – Ebrahim Afshinnekoo – Cell Systems

Food microbiology

Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos – Junichiro Marui – Bioscience of Microbiota, Food and Health

Review: Zooming into food-associated microbial consortia: A “cultural” evolution – Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Bioinformatics

Programming: Pick up Python – A powerful programming language with huge community support – Jeffrey M. Perkel – Nature

Microbes in the news

Podcast: What lived in ancient human intestines? Interview with Jessica Metcalf – The Naked Scientists

Woman becomes obese after fecal transplant from overweight donor – Brooks Hays – UPI

Microbiome linked to type 1 diabetes: Shift in microbiome species diversity prior to disease onset – Science Daily

Gut microbes are good for mood – Xanthe Hunt – LongevityLive

Satire: Five Dead As Pro- and Anti-Microbiome Demonstrators Clash – The Allium

Video: The role of gut bacteria in brain disease – Robert Friedland – YouTube

Book: I, Superorganism – Jon Turney – IconBooks

Big Data and Bacteria: Mapping the New York Subway’s DNA – Robert Lee Hotz – Wall Street Journal

Drug-resistant bacteria lurk in subway stations, high school students discover – Science Daily

Among New York Subway’s Millions of Riders, a Study Finds Many Mystery Microbes – Elizabeth A. Harris – New York Times

Environmental factors may affect how infants’ gut bacteria mature – News Medical

Could Genetically Engineered Bacteria in Your Colon Replace Vitamins? – Sarah Zhang – GizModo

Why Measles Is the Most Contagious Virus – Mandy Oaklander – Time

Busting the 5-second rule: Robot, Petri dishes of bacteria part of science fair – Leigh Guidry – The Town Talk

Not about microbiology, but a very good read: High throughput sequencing for neuroscience – Sean Eddy – Cryptogenomicon

No Bik’s Picks today, sorry guys.

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February 3, 2015

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Pregnancy and birth

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio

Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE

Human oral microbiome

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports

Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology

Human respiratory microbiome

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE

Human gut microbiome

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Animal microbiome

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE

Plant microbiome

Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils

Soil microbiome

Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology

Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry

Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments

Water microbiome

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography

Microbiome of the built environment

Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment

Bioreactor microbiome

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports

Food microbiology

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology

Techniques

PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE

Bioinformatics, metagenomics

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE

In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research

SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics

A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Book: Biocode: The New Age of Genomics

Phages and viruses

Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE

Microbes in the news

The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio

The Human Microbiome and Media Confusion – Science in the News – Harvard

Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos

Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome

Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio

Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients

Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes

Science, publishing, and career

From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog

Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI

A Future Segregated by Science? – Charles M. Blow – New York Times

Bik’s Picks

Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily

Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs

Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press

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January 28, 2015

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I will be traveling to visit family in the upcoming week, so there might not be a post every day. But I will do my best to keep y’all up to date with the microbiome literature. In today’s installment, there are articles about skin microbiome around abscesses, misclassifications of bacteria in Genbank, archaea and rice plant roots. Also, if you like chicken wings with Campylobacter, you should have put some sauce on it.

General microbiome

Crystal Ball: Human microbiota: ‘The philosophers have only interpreted the world in various ways. The point, however, is to change it’ – Harald Brüssow – Microbial Biotechnology

Human skin microbiome

The cutaneous microbiome in out-patients presenting acutely with skin abscesses – James M. Horton – Journal of Infectious Diseases

Animal and other models for microbiome research

In Vitro Investigation of the Effect of Oral Bacteria in the Surface Oxidation of Dental Implants – Sathyanarayanan Sridhar – Clinical Implant Dentistry and Related Research

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice – Xiaofei Xu – PLOS ONE

Animal microbiome

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description of Escovopsis kreiselii sp. nov. – Lucas A. Meirelles – PLOS ONE

Plant microbiome

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols– Sarah Croes – Environmental Microbiology

Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission – Judith Pump – Environmental Microbiology

Soil and rock microbiome

Formation of iron-rich shelled structures by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Water microbiome

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling– Markus V. Lindh – Environmental Microbiology

Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities – Mercè Berga – Environmental Microbiology

Review: Marine Snow: A Brief Historical Sketch – Mary Silver – Limnology and Oceanography Bulletin

Food microbiology

Just in time for the Superbowl: The Antimicrobial Effect of Spice-Based Marinades against Campylobacter jejuni on Contaminated Fresh Broiler Wings – Gintarė Zakarienė – Journal of Food Science

Metagenomics

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database – Roxana Beaz-Hidalgo – PLOS ONE

Metabolomics

Dominant components of the Thoroughbred metabolome characterised by 1H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids – E. E. Escalona – Equine Veterinary Journal

New Techniques

DNA sequencing using ​polymerase substrate-binding kinetics – Michael John Robert Previte – Nature Communications

Single cell biotechnology to shed a light on biological ‘dark matter’ in nature – Wei E. Huang – Microbial Biotechnology

Ecology

Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff – Jue Wang – PLOS Biology

Review: Is successional research nearing its climax? New approaches for understanding dynamic communities – Scott J. Meiners – Functional Ecology

Editorial: Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies – Gabriele Berg – Microbial Biotechnology

Microbes in the news

Skin abscesses displayed distinct cutaneous microbiota – Healio

Stress during pregnancy related to infant gut microbiota – HealthCanal

Fatal peanut allergies could be cured by probiotic bacteria, say Australian doctors – Jonathan Pearlman – The Telegraph

UF researcher gets grant to study probiotics’ effects – Jeff Schweers – Gainesville

Science, publishing and career

Not your average technician: Research relies on unsung heroes working behind the scenes — and some of them have rather unusual jobs – Michael Hopkin – Nature

Career counselling: Pick a path – Neil Savage – Nature

Inclusivity: Mentor matters – Nature

FactChecking Science-based Claims – FactCheck.org
http://www.factcheck.org/2015/01/factchecking-science-based-claims/

Bik’s Picks

Did genetic links to modern maladies provide ancient benefits? – Science Daily

Skull discovery suggests location where humans first had sex with Neanderthals – The Guardian

Spiders Spin Electrically Charged Silk To Make It Sticky – Marissa Fessenden – Smithsonian

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January 20, 2015

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Today we will honor #PenguinAwarenessDay with an older paper, but all others links are brand new. There is the cave microbiome, bacteria in fermented yak milk, and a warning about comparing data obtained in mouse models. Here we go:

Perspective: Where Next for Microbiome Research? – Matthew K. Waldor – PLOS Biology

Review: The Microbiome and Graft Versus Host Disease – Nathan Mathewson, Pavan Reddy – Current Stem Cell Reports

Review: The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill? – Lajos Rózsa – Biology Direct

Review: Prevention of Microbial Communities: Novel Approaches Based Natural Products – George D. Mogosanu – Current Pharmaceutical Biotechnology

Human respiratory microbiome

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome – Arvind Venkataraman – mBio

Review (behind paywall, even at Stanford): Immunology, genetics and microbiota in the COPD pathophysiology: potential scope for patient stratification – Rajneesh Malhotra, and Henric Olsson – Expert Review of Respiratory Medicine

Human gut microbiome

Helicobacter pylori infection as a protective factor against multiple sclerosis risk in females – Marzena J Fabis Pedrini – J Neurol Neurosurg Psychiatry

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers – A Lavelle – Gut

Review: The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases? – Gerardo Nardone, Debora Compare – United European Gastroenterology Journal

Pregnancy and birth

Review: Human Milk: Mother Nature’s Prototypical Probiotic Food? – Michelle K McGuire, and Mark A McGuire – Advances in Nutrition

Animal models of microbiome research

Perspective: How informative is the mouse for human gut microbiota research? – Thi Loan Anh Nguyen – Disease Models & Mechanisms

Attenuated portal hypertension in germ-free mice: Function of bacterial flora on the development of mesenteric lymphatic and blood vessels – Sheida Moghadamrad – Hepatology

High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy – Young Suk Kim – Anaerobe

Antibiotic perturbation: An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile – Matthew Miezeiewski – ISME J

Animal microbiome

This is a 2013 article, but I included it to honor today’s #PenguinAwarenessDay:
Interspecific variations in the gastrointestinal microbiota in penguins – Meagan L. Dewar – MicrobiologyOpen

Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata using functional metagenomics – María Alcaide – Applied and Environmental Microbiology

Plant microbiome

Structure, variation, and assembly of the root-associated microbiomes of rice – Joseph Edwards – PNAS USA

Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri – E. Marie Muehe – Applied and Environmental Microbiology

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics – Martin Grube – ISME J

Soil microbiome

Profiling microbial communities in manganese remediation systems treating coal mine drainage – Dominique L. Chaput – Applied and Environmental Microbiology

Bacterial succession in paddy soils derived from different parent materials – Rong Sheng – Journal of Soils and Sediments

Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization – R. Zornoza – Geoderma

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA# – Swathi A. Turlapati – Frontiers in Microbiology

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust – Alberto Robador – Frontiers in Microbiology

Water microbiome

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean – Mary Thaler and Connie Lovejoy – Applied and Environmental Microbiology

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly – Chuck Pepe-Ranney, Ed Hall – BioRxiv

Catchment-scale biogeography of riverine bacterioplankton – Daniel S Read – ISME J

Microbiome of the built environment

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas – I. Gandolfi – Applied Microbiology and Biotechnology

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes – Yantian Ma – Nature Scientific Reports

A long-term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus – B.A. Potter – Letters in Applied Microbiology

Bioreactor microbiology

Groundwater Chemistry Determines the Prokaryotic Community Structure of Waterworks Sand Filters – Christian N. Albers – Environmental Science & Technology

Impact of Organic Load Shock on the Dynamic Transition of Microbial Communities During the Anaerobic Start-up Process – Jie Li – Energy Procedia

Food microbiology

High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk – Wenjun Liu – Annals of Microbiology

Viruses and phages

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome – Bonnie L Hurwitz – ISME J

BSc thesis: Metagenomic study of the human gut virome during the first year of life – David Mayo Muñoz – Universitat Politecnica de Valencia

Metagenomics

Strong spurious transcription likely a cause of DNA insert bias in typical metagenomic clone libraries – Kathy N Lam, Trevor C Charles – BioRXiv

Commentary: Capturing bacterial chromosome conformation – Andrea Du Toit – Nature Reviews Microbiology

Metabolomics

Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Review: The Role of Colonic Bacteria in the Metabolism of the Natural Isoflavone Daidzin to Equol – Fatemeh Rafii – Metabolites

Microbes in the news

Can the Microbiome Mutiny? – Carl Zimmer – National Geographic

Fast-Paced Microbiome (about Rob Knight) – Genome Web

Researchers urge caution in studies of mice and microbes – Sarah DeWeerdt – SFARI

Gut microbes trigger autoimmune disease later in life in mice – Science Codex

Ulcer Bacteria Tied to Lower Multiple Sclerosis Risk in Women – HealthDay

Breweries partner with bacteria-detecting Philadelphia start-up – Diane Mastrull – Philly.com

New Species Discovered Beneath Ocean Crust – Robert Perkins – Pressroom USC

Ancient Viruses Gain New Functions in the Brain – Andrea Alfano – Scientific American

Science, publishing, and career

Is it Ph.D. or PhD? And are PhDs who act like MDs a special kind of douchebag? Twitter debates – Chris Seper – MedCityNews

Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? – Julie K. Pfeiffer – mBio

Don’t be that dude: Handy tips for the male academic – Tenure She Wrote

Science and art

Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu – Jonathan Eisen – The Tree of Life

Bik’s Picks

Exercise at depth alters bradycardia and incidence of cardiac anomalies in deep-diving marine mammals – Terrie M. Williams – Nature Communications

What’s Up With That: Birds Bob Their Heads When They Walk – Nick Stockton – Wired

Over 80 percent of Americans support “mandatory labels on foods containing DNA” – Ilya Somin – Washington Post

The Discoloration of the Taj Mahal due to Particulate Carbon and Dust Deposition – M. H. Bergin – Environmental Science & Technology

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January 19, 2015

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Thanks for all the encouraging comments here and per email! This blog appears to fill an important niche in the coverage of scientific microbiome research, in a wide range of hosts and environmental sources, so I will continue writing this. But please spread the word – 100 viewers per day is nice, but more is better!

As one of the commenters suggested, I will try to mark Reviews as such, so they are easier to find (or skip).

Here we go with a new post. It’s Monday, so there is a lot to cover.

Human oral microbiome

Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile – Tacíria M Bezerra – Journal of Clinical Pathology

Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron – Pamela Vazquez-Gutierrez – BMC Microbiology

Review: Tuning the Brain-Gut Axis in Health and Disease – Rainbo Hultman – Current Stem Cell Reports

Microbiome of pregnancy and birth

Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques – Roberto Romero – Journal of Perinatal Medicine

Review: Relationship between periodontal diseases and preterm birth: Recent epidemiological and biological data – Moneet Walia, Navdeep Saini – International Journal of Applied and Basic Medical Research

Review: Viral Infections During Pregnancy – Michelle Silasi – American Journal of Reproductive Immunology

Review: Stress and the Commensal Microbiota: Importance in parturition and infant neurodevelopment – Tamar L. Gur – Frontiers in Psychiatry

Animal models of microbiome research

Commensal microbiota influence systemic autoimmune responses – Jens T Van Praet – The EMBO Journal

Modulation of the Intestinal Microbiota Is Associated with Lower Plasma Cholesterol and Weight Gain in Hamsters Fed Chardonnay Grape Seed Flour – Hyunsook Kim – J. Agric. Food Chem

Dysbiotic bacteria translocate in progressive SIV infection – Z Klase – Mucosal Immunology

Animal microbiome

Comparison of the gut microbiomes of 12 bony fish and 3 shark species – Carrie E. Givens – Marine Ecology Progress Series

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation – Jian Xue – Genome Biology

Review: Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota – Michael Poulsen – Environmental Microbiology

Plant microbiome

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root associated fungi mirrors plant succession in two glacial chronosequences – Marie Davey – Environmental Microbiology

Book: Beneficial Plant-Bacterial Interactions – Bernard R. Glick

Soil and sediment microbiome

Soil Bacterial Communities are Shaped by Temporal and Environmental Filtering: Evidence from a Long-Term Chronosequence – Zachary Freedman and Donald R. Zak – Environmental Microbiology

Abstract: Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois – Alexander B Faulkner – Proceedings, 19th Central Hardwood Forest Conference; 2014 March

Bacterial community composition at anodes of microbial fuel cells for paddy soils: the effects of soil properties – Ning Wang – Journal of Soils and Sediments

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Soil-Borne Microbiome: Linking Diversity to Function – Lucas W. Mendes – Microbial Ecology

Phytoextraction of nickel and rhizosphere microbial communities under mono- or multispecies hyperaccumulator plant cover in a serpentine soil – Marie Rue – Australian Journal of Botany

Methane-derived carbon flow through microbial communities in arctic lake sediments – Ruo He – Environmental Microbiology

Review: Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations – Sheree J. Finley – Applied Soil Ecology

Water microbiome

Book (open access): Subseafloor Biosphere Linked to Hydrothermal Systems
Some chapters of interest:
– Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor in the Back-Arc Hydrothermal System of the Southern Mariana Trough – Shingo Kato
– Microbial Cell Densities, Community Structures, and Growth in the Hydrothermal Plumes of Subduction Hydrothermal Systems – Michinari Sunamura, Katsunori Yanagawa
– Comparative Investigation of Microbial Communities Associated with Hydrothermal Activities in the Okinawa Trough – Ken Takai, Satoshi Nakagawa
– Quantification of Microbial Communities in Hydrothermal Vent Habitats of the Southern Mariana Trough and the Mid-Okinawa Trough – Katsunori Yanagawa

Microbiome of the built environment

Review: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome – Brent Stephens – Indoor Air

Food microbiology

Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese – Luana Faria Silva – Journal of Food Science

Metagenomics

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data – Xutao Deng – Nucleic Acids Research

Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology

Metabolomics, transcriptomics, and proteomics

Effects of high fructose and salt feeding on systematic metabonome probed via 1H NMR spectroscopy – Yongxia Yang – Magnetic Resonance in Chemistry

Also see above: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome – Florence Privé – Applied Microbiology and Biotechnology

Review: Proteomics of hosts and pathogens in cystic fibrosis – Karthik Shantharam Kamath – Proteomics – Clinical Applications

Bioinformatics

Book chapter: e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling – Fosso Bruno – RNA Bioinformatics / Methods in Molecular Biology

Book chapter: Deciphering Metatranscriptomic Data – Evguenia Kopylova – RNA Bioinformatics / Methods in Molecular Biology

Amplification and sequencing techniques

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples – Marta Pawluczyk – Analytical and Bioanalytical Chemistry

Probiotics

Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model – Tomohiro Kawahara – Microbiology and Immunology

Microbes in the news

* One Scientist’s Race To Help Microbes Help You – Katherine Harmon Courage – NPR Shots

Researchers reveal link between the microbiome of young mice and later onset of autoimmune disease – News Medical

Podcast: Do Gut Bacteria Tell Us What To Eat? – Beth Anne Austein / The Food Guys – Montana Public Radio

The Fungus in Your Cheese Is Having Weird Sex – Rose Eveleth – Smithsonian.com

Disturbed gut microbiome linked to Parkinson’s disease – News Medical

#BacteriaHysteria

Honoring last week’s Law Enforcement Appreciation Day: Sheriff’s Office gets bacteria cleanse – Richard Goad – Cleveland Banner

Science, publishing, and career

7 Tips for Women at Science Conferences – Hilda Bastian – PLOS Blogs

Bik’s Picks

Do 80% of Americans not know there’s DNA in food? – Ben Lillie blog

Researchers Who Provided Key Evidence For Gluten Sensitivity Have Now Thoroughly Shown That It Doesn’t Exist – Jennifer Welsh – Business Insider

This whale might be old, but it does not look too happy (or it is swimming upside down?)
The Secret To Living 200 Years? Ask A Whale – Paul Rodgers – Forbes.com

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