Category Archives: Fecal Transplants

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 10, 2015

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Microbiome of pregnancy and birth

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan (Sam) Ma – Scientific Reports

Human respiratory microbiome

The nasal microbiota in health and disease: variation within and between subjects – Kristi Biswas – Frontiers in Microbiology

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis – Won Hee Jung – Mycoses

Human oral microbiome

Review: Salivary Diagnostics and the Oral Microbiome – Jennifer E. Kerr – Advances in Salivary Diagnostics

Review: Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses – Georgios Charalampakis – Virulence

Review: On the dynamics of root canal infections – what we understand and what we don’t – Matthias Zehnder – Virulence

Human gut microbiome

See also Rojo paper under Metabolomics

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences – Brett Wagner Mackenzie – Frontiers in Microbiology

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease – Weiwei Jiang – Scientific Reports

Intestinal Lesions Are Associated with Altered Intestinal Microbiome and Are More Frequent in Children and Young Adults with Cystic Fibrosis and Cirrhosis – Thomas Flass – PLOS ONE

The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing – LY Kwok – Beneficial Microbes

Review: Contribution of diet to the composition of the human gut microbiota – Daniela Graf – Microbial Ecology in Health and Disease

Animal microbiome

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing – Edward Alain B. Pajarillo – Asian-Australasian Journal of Animal Sciences

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Abstract: Bugs in bats 2: Analysis of microbial communities in faecal samples obtained from bats in the Netherlands – JCM Wolkers-Rooijackers – 11th Conference of the Dutch Society for Wildlife Health

Plant microbiome

Rapid quantification of rice root-associated bacteria by flow cytometry – G. Valdameri – Letters in Applied Microbiology

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria – Kiwamu Minamisawa – Frontiers in Microbiology

Characterization of Leaf Blade- and Leaf Sheath-Associated Bacterial Communities and Assessment of Their Responses to Environmental Changes in CO2, Temperature, and Nitrogen Levels under Field Conditions – Seishi Ikeda – Microbes and Environments

Soil, sediment, and rock microbiome

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice – J. J. Elser – Applied and Environmental Microbiology

Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils – Ning Wang – FEMS Microbiology Ecology

Analysis of Sclerotia-Associated Fungal Communities in Cool-Temperate Forest Soils in North Japan – Anzilni F. Amasya – Microbes and Environments

Water microbiome

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year – M. Korlević – Applied and Environmental Microbiology

Viruses and phages

Traces of ATCV-1 associated with laboratory component contamination – Kristín Rós Kjartansdóttir – PNAS USA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination – Robert H. Yolken – PNAS USA

Microbial Ecology

Temporal patterns of rarity provide a more complete view of microbial diversity – Ashley Shade, Jack A. Gilbert – Trends in Microbiology

Metagenomics

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics – Carolina Megumi Mizuno – mBio

Metabolomics

Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases – David Rojo – Scientific Reports

Review: Animals in a bacterial world: opportunities for chemical ecology – Alexandra M. Cantley and Jon Clardy – Natural Product Reports

Bioinformatics

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies – Mohamed Mysara – Applied and Environmental Microbiology

Techniques

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – MicroBEnet

More microbes

Natural Green Coating Inhibits Adhesion of Clinically Important Bacteria – Danielle S. Trentin – Scientific Reports

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

Breastfeeding prepares a baby for solid food – Tim Sandle – Digital Journal

Gut microbiota reveal better ways of detecting (and preventing) colorectal cancer – Kristina Campbell – Microbiome Institute

Our Inner Viruses: Forty Million Years In the Making – Carl Zimmer – National Geographic

Our wine owes a debt to ancient viruses – Andrew Geering – Phys.org

Diet is the Chief Factor Behind Gut Microbiome Diversity, Study Shows – Patricia Inacio – IBD News Today

Citizen Oceanography Meets the Marine Microbiome – Rachelle Lauro – Mission Blue

Fecal Microbiota Transplants: An Insider’s Guide – Monica J. Smith

Science and Art

Researcher Determined to Play Piano Duet With Yellow Slime Mold – The Mary Sue

And the winners of the #spacemicrobes Microbial Playoffs are… – Arvind Suresh – Discover Magazine

A Beautiful Wallpaper Made With Smallpox Vaccine – Joseph Flaherty – Wired.com

Bik’s Picks
Stressed Young Bees Linked To Colony Collapse – Jim Algar – Tech Times

Meet Spot: New Breed of Robot Dog Climbs and Trots – Elizabeth Palermo – Live Science

Australia’s Shocking Rate Of Mammal Extinction Blamed On Cats And Red Foxes Brought Over By European Settlers – Rebekah Marcarelli – Headlines and Global News

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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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