Category Archives: Fecal Transplants

January 14, 2017

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So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

January 11, 2017

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Vaginal microbial  communities associated with HIV acquisition or protection, evolution and function of the appendix, microbes and bird evolution, soil microbes followed for 17 years, and bone microbiome and cause-of-death of an 18th century child.
Jobs

Faculty Position in Microbiome Research – National University of Singapore – Science Careers

Pregnancy and early life

The Role of Early Life Nutrition in the Establishment of Gastrointestinal Microbial Composition and Function – Erin C. Davis – Gut Microbes

Human vaginal microbiome

* Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity

Diagnosis and microecological characteristics of aerobic vaginitis in outpatients based on preformed enzymes – Zhi-liang Wang – Taiwanese Journal of Obstetrics & Gynecology

Human respiratory microbiome

Review: The microbiome in mechanically ventilated patients – Yin, Yudong – Current Opinion in Infectious Diseases

Human gut microbiome

* Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol

Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases – Abbas Kazerouni – PLOS ONE

Review: Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response – Allison Clark – Frontiers in Immunology

Review: Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Animal experiments

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior – Caleb Fischer – eLIFE

Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin – Xue Xiao – Scientific Reports

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change – P. Grimm – Animal

Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea – Samir Dou – PLOS ONE

Animal microbiome

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum – A.V. Nedoluzhko – Genomics Data

* Review: Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history – Jessica K. Evans – Hormones and Behavior

Archaeology microbiome

* The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing – Valeria D’Argenio – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds – Shigenobu Yoshida – Journal of Photochemistry and Photobiology B: Biology

Major Crop Species Show Differential Balance between Root Morphological and Physiological Responses to Variable Phosphorus Supply – Yang Lyu – Frontiers in Plant Science

* Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Water and extremophile microbiome

Two microcrustaceans affect microbial and macroinvertebrate-driven litter breakdown – Sophie Chambord – Freshwater Biology

Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes – Adam H Stevens – bioRxiv Preprint

Bioinformatics, statistics, and metagenomics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer – Aaron Weimann – mSystems

Structural zeros in high-dimensional data with applications to microbiome studies – Abhishek Kaul – Biostatistics

More microbiology

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response – Robert Heler – Molecular Cell

Press: Researchers Learn to Enhance Bacteria’s Ability to Form Genetic Memories – SciCasts

Microbes in the news
Meet Canada’s ‘poop lady’: “I got to know people up there very well over the years, said Girard, 28. – EurekAlert

A new year for our journal club! – Fiona Whelan – Human Microbiome Journal Club

Oral bacteria linked to preterm labor in Hawaiʻi – Desiree Uyeda – University of Hawai’i News

Mayo’s microbiome study targets diabetes – Brett Boese – Post Bulletin

MicrobEYEome: Liver Cancer Patients Have a Signature Microbiome – GastroEndo News

Presentation: The role of the microbiome in Porcine Reproductive & Respiratory Syndrome (PRRS) – Megan Niederwerder – YouTube

Based on the title this appears to be a good candidate for the “Overselling The Microbiome Award” by Jonathan Eisen: How Sexual Attraction Is Shaped by Gut Bacteria, Infectious Diseases, and Parasites – Kathleen McAuliffe – BigThink

Latest Dengue Update: Bacteria Strain That Stops Dengue Transmission In Mosquitoes Dies In Hot Environment – Minnow Blythe – Counsel Heal

Microbes on the market

Allergan (AGN) Enters Licensing Agreement with Assembly Biosciences (ASMB) to Obtain Worldwide Rights to GI Programs – StreetInsider

Ferring Partners with Intralytix to Develop Bacteriophage Treatments for Conditions Associated with the Microbiome and Drug-Resistant Bacteria – BusinessWire

La Roche-Posay Introduces Prebiotic Skincare Line – PR NewsWire

Indigo’s Preliminary Commercial Data Demonstrate Significant Yield Gains for Growers with Plant Microbiome Product – PR NewsWire

Bik’s non-microbiology picks

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study – Mustafa Chopan – PLOS ONE

January 5, 2017

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Microbiome of Inuit, centenarians, microbes showing differential expression when they are grown with sound, taxonomy of prokaryotic viruses.

Human gut microbiome

* Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere

* The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile – Biagi Elena – Mechanisms of Ageing and Development

Review: Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota – Jun Xu – Medicinal Research Reviews

Editorial: The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation – Daniel van der Lelie – Microbial Biotechnology

Animal experiments

Effect of dietary kefir on the growth performance, feed utilization and fatty acid profile of juvenile rainbow trout, Oncorhynchus mykiss – E. Gümüş – Aquaculture Nutrition

Plant, root, and soil microbiome

The Pseudomonas putida T6SS is a plant warden against phytopathogens – Patricia Bernal – The ISME Journal

Mycorrhizal Colonization Status and Rhizosphere Soil Properties of BCSIR Reserve Forest Rajshahi, Bangladesh – M. Halder – Current World Environment

Waste and pollution microbiology

Batch and continuous removal of heavy metals from industrial effluents using microbial consortia – F. Migahed – International Journal of Environmental Science and Technology

Musical microbes

* Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz – Chinmayi Joshi – bioRxiv

Bioinformatics

Book: Molecular Data Analysis Using R – Csaba Ortutay

Viruses and phages

* Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee – Evelien M. Adriaenssens – Archives of Virology

Metabolomics

Optimal allocation of metabolic functions among organisms in a microbial ecosystem – Qi Zhao – Decision and Control (CDC), 2016 IEEE 55th Conference on

Microbes in the news

CDC keeps secret its mishaps with deadly germs: CDC blacked-out information from lab incident reports – Alison Young – USA Today

Single fecal transplant no more effective than standard of care in treating C. diff – MedicalXpress

Alaska gulls are picking up antibiotic-resistant bacteria that could infect humans – Yereth Rosen – ADN

Man-made lake near Linganore drained to kill toxic pink bacteria: pink-colored cyanobacterium releases a toxin – Samantha Hogan – The Frederick News Post

Bacteria Hysteria

Dirty Money. The public health case for a cashless society – Dina Fine Maron – Scientific American
The Money in Your Wallet Might Be Covered With Poop, Mold, and Cocaine – Brad
– Money
The 5 Dirtiest Things You Touch Every Day – Markham Heid – Time

Microbes in the market

Israeli Gut Microbiome Startup Lands Mayo Clinic Venture Backing – TwinCities Business

Ritter Pharmaceuticals Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published in Proceedings of the National Academy of Sciences – Yahoo

Cambridge BioMarketing Announces Five Predictions for 2017 – Yahoo

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business – PR Newswire

Science integrity

Bavarian court sentences me to prison if I dare repeat unwelcome facts of Walles’ trachea transplants – Leonid Schneider – For Better Science

 

December 30, 2016

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Vancomycin treatment preceding fecal transplantation, a diet for IBD, dieting and gut microbiome diversity, halotolerant extremophiles for recycling pollutants, mass spectrometry on medical swabs.

Human vaginal microbiome

Genital injury signatures and microbiome alterations associated with depot medroxyprogesterone acetate usage and intravaginal drying practices – Kenzie D. Birse – The Journal of Infectious Diseases

Human gut microbiome

Oral Vancomycin Followed by Fecal Transplantation Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An Open-Label, Randomized Controlled Trial – Susy S. Hota – Clinical Infectious Diseases

Fecal Fixation: Fecal Microbiota Transplantation for Clostridium difficile Infection – Stuart Johnson – Clinical Infectious Diseases

SCD diet: Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease – David L. Suskind – Journal of Clinical Gastroenterology

Press: Changes With Diet Therapy in Active Inflammatory Bowel Disease – Science Daily

Review: From bugs to brains: The microbiome in neurological health – Kyla A. McKay – Multiple Sclerosis and Related Disorders

Animal experiments

Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions – Nicholas W. Griffin – Cell Host & Microbe

Press: Your Crappy American Diet Might Leave Your Gut Bacteria Stunted – Ryan F. Mandelbaum – Gizmodo
Your microbiota’s previous dining experiences may make new diets less effective – EurekAlert

Intestinal Serotonin Transporter Inhibition by Toll-Like Receptor 2 Activation. A Feedback Modulation – Eva Latorre – PLOS ONE

Press: Gut microorganisms affect our physiology – EurekAlert

Alterations in the gut microbiota can elicit hypertension in rats – Sareema Adnan – Physiological Genomics

Plant, root, and soil microbiome

Impact of plant growth-promoting rhizobacteria on root colonization potential and life cycle of Rhizophagus irregularis following co-entrapment into alginate beads -P. Loján – Journal of Applied Microbiology

Review: Soil Bacteria Alter Plant Physiology to Mitigate Salinity Stress Effects in Glycophytes – Ramalingam Radhakrishnan – Frontiers in Plant Science

Presentation abstract: Soil microbial community structures and activities in relation to nitrogen cycling in two contrasting soils in Malawi – community responses to added carbon – Akane Chiba – International Nitrogen Initiative

Waste and pollution microbiology

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations
– Chuan Chen – Chemosphere

Microbiological water quality in the medical device industry in Italy – Emilio D’Ugo – Microchemical Journal

Halotolerant extremophile bacteria from the Great Salt Lake for recycling pollutants in microbial fuel cells – Matteo Grattieri – Journal of Power Sciences

Functionality of microbial communities in constructed wetlands used for pesticide remediation: Influence of system design and sampling strategy – Tao Lv – Water Research

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies – Arghya Mukherjee – bioRxiv

Food microbiology

Saccharomyces uvarum is Responsible for the Traditional Fermentation of Apple CHICHA in Patagonia – ME Rodríguez – FEMS Yeast Research

Metabolomics

Medical swab analysis using desorption electrospray ionization mass spectrometry (DESI-MS) – a non-invasive approach for mucosal diagnostics – Pamela Pruski – Analytical Chemistry

Coping with inevitable accidents in metabolism – Antoine Danchin – Microbial Biotechnology

Techniques

Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing – Morag Taylor – Journal of Clinical Pathology

Microbes in the news

Short podcast: Academic Minute – Diversifying Your Microbiome. Jack Gilbert details how the sharing of bacteria from person to person could make us healthier in the long run. – Inside Higher Ed

Ancient ‘Eternal Life’ bacteria leaves Russian scientist ‘Illness-Free’ – Harry Walker – Express

Bacteria evolution offers insights into human protein interactions – Brooks Hays – UPI

High school students discover new phages: Genomics research gives youth a leg up on education – Tonya S. Grace – Kentucky New Era

Fermentation expert Sandor Katz on why we shouldn’t fear bacteria – Andrew Sun – SCMP

Novel diet therapy helps children with crohn’s disease and ulcerative colitis reach remission – Science Daily

Prebiotics for your skin: The La Roche-Posay Toleriane Double Repair Moisturizer Could Be the Secret to Better Skin – Sarah Kinonen – Allure

December 23, 2016

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Resistant starch diets, mass spectrometry imaging, viruses in coral health and disease, mitochondrial and chloroplast blocking clamps to identify plant-associated microbiomes, vitamin D and the gut, microbes in pores, uBiome Microbiome Impact Grant winner.

Pregnancy and early life

Starter formula enriched in prebiotics and probiotics ensures normal growth of infants and promotes gut health: a randomized clinical trial – Michael Radke – Pediatric Research

Human skin microbiome

The balance of metagenomic elements shapes the skin microbiome in acne and health – Emma Barnard – Scientific Reports

Microbiome of nearly sterile sites

Correspondence: Blood microbiota as a potential non-invasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully – Zongxin Ling – Hepatology

Human gut microbiome

 * Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk – Nathalie Bergeron – British Journal of Nutrition

Fecal Microbiota Transplant in Severe and Severe-Complicated Clostridium difficile: A Promising Treatment Approach – Monika Fischer – Gut Microbes

Evaluation of clinical safety and beneficial effects of stachyose-enriched α-galacto-oligosaccharides on gut microbiota and bowel function in humans – Ting Li – Food & Function

Low abundance of colonic butyrate-producing bacteria in HIV infection is associated
with microbial translocation and immune activation – Stephanie M. Dillon – AIDS

Meta-analysis: Pretreatment with antibiotics may enhance the efficacy of fecal microbiota transplantation in ulcerative colitis: a meta-analysis – A H Keshteli – Mucosal Immunology

Meta-analysis: Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis – Yingting Zhou – BioMed Research International

Viewpoint: The Microbiome and Risk for Obesity and Diabetes – Anthony L. Komaroff – JAMA

Review: The Impact of the Gut Microbiota on Humoral Immunity to Pathogens and Vaccination in Early Infancy – Quang N. Nguyen – PLOS Pathogens

Review: Microbiota and prebiotics modulate uremic toxins generation – Laetitia Koppe – Panminerva Medica

Review: Influence of nutrition therapy on the intestinal microbiome – Monika A. Krezaleka

Review: A Possible Role of Intestinal Microbiota in the Pathogenesis of Ankylosing Spondylitis – Lianjun Yang – Int J Mol Sci

Review: Food allergy and the gut – Anna Nowak-Wegrzyn – Nature Reviews Gastroenterology & Hepatology

The Gut Microbiome and the Liver, special issue of Seminars in Liver Disease with lots of reviews:

 

Animal experiments

Western diet induces colonic nitrergic myenteric neuropathy and dysmotility in mice via saturated fatty acid- and LPS-induced TLR4 signaling – François Reichardt – Journal of Physiology

* Vitamin D Signaling through Induction of Paneth Cell Defensins Maintains Gut Microbiota and Improves Metabolic Disorders and Hepatic Steatosis in Animal Models – Danmei Su – Frontiers in Physiology

Vitamin D Improves Gut Microbiota, Study Finds – Sci-News

Animal microbiome

* Review: The role of viruses in coral health and disease – Michael Sweet – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment – Zhi P. Ma – Frontiers in Microbiology

Bioaccumulation of metals in reeds collected from an acid mine drainage contaminated site in winter and spring – Lin Guo – Environmental Technology

* Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery – Sara L. Jackrel – Molecular Ecology Resources

* Microbial competition in porous environments can select against rapid biofilm growth – Katharine Z. Coyte – PNAS

Water microbiome

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation – E. D. Beaton – Frontiers in Microbiology

Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia – Yanhong Wang – Frontiers in Microbiology

Disturbance Increases Microbial Community Diversity and Production in Marine Sediments – Pierre E. Galand – Frontiers in Microbiology

Waste and pollution microbiology

Seafood-Processing Sludge Composting: Changes to Microbial Communities and Physico-Chemical Parameters of Static Treatment versus for Turning during the Maturation Stage – Iria Villa – PLOS ONE

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly – James S Griffin – The ISME Journal

Metabolomics

* Mass Spectrometry Imaging of Complex Microbial Communities – Sage J. B. Dunham – Accounts Chemical Research

Techniques

* Mitochondrial and chloroplast blocking clamps: Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery – Sara L. Jackrel – Molecular Ecology Resources

Microbial ecology

Probabilistic adaptation in changing microbial environments – Yarden Katz – PeerJ

Microbes in the news

* UCSF Researcher to Investigate Diabetes and the Microbiome in Filipino Populations with uBiome Microbiome Impact Grant – PR Web

An interesting year – Nature Microbiology

Microbiota: Reseeding the gut – Liam Drew – Nature

Danish researchers uncover bacteria’s secret code language – News Medical

New CRISPR-Cas Enzymes Discovered – Kerry Grens – The Scientist

Move over Cas9, CRISPR-Cas3 might hold the key to solving the antibiotics crisis – Sarah Buhr – Tech Crunch

Gut bacteria may hold key to treating autoimmune diseases – EurekAlert
The Secret To Treating Autoimmune Disease May Lie In The Gut – The Huffington Post

Science, publishing and career

The lives they lived: Ruth Hubbard. She was grateful simply to be a female biologist — until she got mad about needing to be grateful – Sara Corbett – New York Times

 

December 21, 2016

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Fluorescence in the mouth, stool transplant with own stool sometimes works too, Clostridium difficile and nutritional niches in the mouse, bacterioplankton metabolism in the Dead Zone, and the invisible Esther Lederberg.

General microbiome

Review: The microbiome in health and disease: a new role of microbes in molecular medicine – Ingo B. Autenrieth – Journal of Molecular Medicine

Human mouth microbiome

Red and Green Fluorescence from Oral Biofilms – Catherine M. C. Volgenant – PLOS ONE

Characterization of saliva microbiota’s functional feature based on metagenomic sequencing – Fang Yang – SpringerPlus

Human respiratory microbiome

Characterization of microbiome in bronchoalveolar lavage fluid of patients with lung cancer comparing with benign mass like lesions – Sang Hoon Lee – Lung Cancer

Human gut microbiome

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation – Christopher Staley – mBio

Press: Study provides clues to improving fecal microbiota transplantation – MedicalXpress

Review: Fecal microbiota transplantation for multiple organ dysfunction syndrome – Nathan J. Klingensmith – Critical Care

Review: Tuning constitutive and pathological inflammation in the gut via the interaction of dietary nitrate and polyphenols with host microbiome – Bárbara S. Rocha – The International Journal of Biochemistry & Cell Biology

Review: Redox signaling mediated by the gut microbiota – Rheinallt M. Jones – Free Radical Biology and Medicine

Editorial: The gut microbiota and immune-regulation: the fate of health and disease –
Eliana Mariño – Clinical Translational Immunology

Animal experiments

Collateral Damage: Detrimental Effect of Antibiotics on the Development of Protective Immune Memory – Joseph M. Benoun – mBio

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments – Matthew L Jenior – bioRxiv

Water microbiome

Decoding bacterioplankton metabolism in the northern Gulf of Mexico Dead Zone – J. Cameron Thrash – bioRxiv

Built environment microbiome

Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists – Maximilian Mora – Microbiome

Phages and viruses

Not sure if this is such a good idea…. Application of Bacteriophage-containing Aerosol against Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit – Yu-Huai Ho – PLOS ONE

Microbial ecology

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System – Sean M. Gibbons – mBio

Microbes in the news

Will Microbiome Board Game Become Infectious? – Gastroenterology & Endoscopy News

Appointment of New Features Editor: Melanie Blokesch – Molecular Microbiology

Microbiomes mix it up – Larrie Stone – Washington County Enterprise

Invisible Esther: the ‘Other’ Lederberg – Walt Nakonechny

DNA markers distinguish between harmless, deadly bacteria. Large genome study IDs potential virulence factors to discriminate new species – Science Daily

Researchers Use Genomic Analysis to Study the Deadly Bacteria Responsible for “Rabbit Fever” – David Jennings – Natural Science News

Prostate cancer drug based on sea-bed bacteria brings complete remission for half of patients – Sarah Knapton – Telegraph

New Laser Treatment Based On Deep-Sea Bacteria Effectively Treats Prostate Cancer – IFL Science

Laser therapy leaves no sign of prostate cancer in 50% of trial patients – John von Radowitz – Independent

How bacteria survive antibiotic treatment – Science Daily

Mouthwash May Kill Gonorrhea Bacteria – Sara G. Miller – LiveScience

Video about resistant starch with nice visualizations: The Hungry Microbiome – Data61

Video: Saving Atlantis: The global coral microbiome project in the Red Sea – Science 360

Happy Holidays from Microbiology Lab – Maria Anne – Clinical Laboratory Blogspot

Microbes on the market

Evolve BioSystems Successfully Defends European Patent Opposition by Danone, Maintaining Their Position as Leaders in the Infant Gut Microbiome Space – Market Wired

November 23, 2016

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Why You Should Probably Be Glad You’re Not a Brown Bear or an Edible Dormouse – Julie Taylor – uBiome blog

“Thankfully, when you have your own microbiome analyzed by uBiome, you’ll be relieved to know that we won’t be sending round a guy in a helicopter with a tranquilizer gun. All you need to do is lightly swab a piece of used toilet paper.”

Human gut microbiome

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection – Stephan J. Ott – Gastroenterology

Research highlight: Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Review: Candida albicans cell-type switching and functional plasticity in the mammalian host – Suzanne M. Noble – Nature Reviews Microbiology

Review: Gut Bacteria and Hydrogen Sulfide: The New Old Players in Circulatory System Homeostasis – Lenka Tomasova – MDPI Molecules

Microbiology of nearly sterile sites

Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome – Kema Malki – PLOS ONE

Animal experiments

Eye of the Finch: Characterization of the Ocular Microbiome of House Finches in Relation to Mycoplasmal Conjunctivitis – Courtney A. Thomason – Environmental Microbiology

Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences – Jennifer Kelly – Environmental Microbiology

Heat Stress Affects Facultative Symbiont-Mediated Protection from a Parasitoid Wasp – Eleanor R. Heyworth – PLOS ONE

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium – Sandrine Brugiroux – Nature Microbiology

Assessment of the Fecal Microbiota in Beef Calves – J.S. Weese – Journal of Veterinary Internal Medicine

The role of microbiota in compensatory growth of protein-restricted rats – Yizhi Zhu – Microbial Biotechnology

Animal microbiome

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host – Juan E. Palomares-Rius – Molecular Ecology

Plant, root, and soil microbiome

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants – Abdul Samad – Environmental Microbiology

Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere – Laura J. White – Environmental Microbiology

Water and extremophile microbiome

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean – Wenxue Wu – Environmental Microbiology

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount – Jarrod J. Scott – Environmental Microbiology

Probing the evolution, ecology and physiology of marine protists using transcriptomics – David A. Caron – Nature Reviews Microbiology

Food microbiology

High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process – Chao Yang – Journal of Food Science

Microbes in the news

Set of 12 microbiology postcards – PREORDER – Microbes and Molecules sciart card set featuring bacteria and fungi, gift for scientist – The Vexed Muddler – Etsy.com

Traces of antibiotic-resistant bacteria have been found in polluted city air. Not good – David Nield – ScienceAlert

Why Sprouts Are Especially Good At Harboring Dangerous Bacteria – Sara G. Miller – LiveScience / Huffington Post

Infectious Diseases Keep Delivering Surprises To The U.S. – Katherine Hobson – NPR

UVA Microbiologist Expands His Research Across the Atlantic – University of Virginia

By Wagging its ‘Tail,’ Bacteria Common in CF Lung Infections May Initiate Immune Reaction – Joana Fernandes – Cystic Fibrosis News Today

‘In five years this will be routine’: Map My Gut start-up offers personalised microbiome advice – Annie-Rose Harrison-Dunn – NutraIngredients

Can bacteria in yogurt calm your anxiety? – Jeff Sossamon – Futurity

September 15, 2016

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A review on the human skin microbiome, review on therapeutic manipulation of microbiotas, and microbial enzymes around earthworm casts.

Jobs and events

Faculty Positions in Microbiology and Immunology – University of South Alabama College of Medicine

Human respiratory microbiome

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum on Allergy & Rhinology

Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation – Kirsty M. Sands – Journal of Critical Care

Human skin microbiome

Review, will be open access soon: Experimental metagenomics and ribosomal profiling of the human skin microbiome – Pamela Ferretti – Experimental Dermatology 

Human gut microbiome

Gut microbiome alterations in patients with stage 4 hepatitis C – AbdelRahman Mahmoud Aly – Gut Pathogens

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Review: Therapeutic Manipulation of the Microbiota: Past, Present and Considerations for the Future – Vincent B. Young – Clinical Microbiology and Infection

Animal experiments

Effects of different diets on intestinal microbiota and nonalcoholic fatty liver disease development – Jian-Ping Liu – World Journal of Gastroenterology

Sex-specific effects of docosahexaenoic acid (DHA) on the microbiome and behavior of socially-isolated mice – Daniel J. Davis – Brain, Behavior, and Immunity

Animal microbiome

Structural differences in gut bacteria communities in developmental stages of natural populations of Lutzomyia evansi from Colombia’s Caribbean coast – Rafael José Vivero – Parasites & Vectors

Plant, root, and soil microbiome

Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts – Jerzy Lipiec – Frontiers in Microbiology

Air microbiome

Influence of Rain on the Abundance and Size Distribution of Bioaerosols –
Chathurika M. Rathnayake – Atmospheric Chemistry and Physics Discussions

Techniques

Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias – Michelle M. O’Donnell – Journal of Microbiological Methods

Application of Next Generation Sequencing Technologies in Revealing Plant-Microbe Interactions – Ramesh Kothari – Journal of Next Generation: Sequencing & Applications

Technical note: Discard the specimen collection swab directly at point of care to improve extensive automated processing in clinical microbiology laboratories – Manuela Avolio – Journal of Microbiological Methods

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janabi – Journal of Microbiological Methods

Microbes in the news

Secrets of life in the soil.Diana Wall has built a career on overturning assumptions about underground ecosystems. Now she is seeking to protect this endangered world – Rachel Cernansky – Nature

Ice machine, sinks linked to Legionnaires’ cases at UW Medical Center – JoNel Aleccia – Seattle Times

Israeli product that pinpoints viruses, bacteria gets European grant – ImmunoXpert is based on the fact that viruses and bacteria stimulate different protein pathways when they infect the body – Judy Siegel-Itzkovich – Jpost.com

A spoonful of sugar helps the bacteria go down. Gel-like layers protect microbes and help them stick to your intestines – Sara Chodosh – Popsci

Bik’s non-microbiology Picks

VA Palo Alto’s spending on artwork blasted – Jacqueline Lee – The Mercury News

 

September 9, 2016

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Microbiome and tuberculosis, mangoes, lessons from amphibians, and the microbiome of buildings.

Human gut microbiome

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection – Ilan Youngster – BMC Medicine

Review: Microbiome Changes during Tuberculosis and Antituberculous Therapy – Bo-Young Hong – Clinical Microbiology Reviews

No consensus on how the microbiome affects tuberculosis, review finds – Science Daily

Animal models

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Mango, “hedgehog” style – Wikipedia

Mango Supplementation Modulates Gut Microbial Dysbiosis and Short-Chain Fatty Acid Production Independent of Body Weight Reduction in C57BL/6 Mice Fed a High-Fat Diet – Babajide Ojo – Journal of Nutrition

Mango and the Microbiota: New Research Reveals Potential Role of this Superfruit in Maintaining Gut Health – National Mango Board – PR Newswire

Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats – Hirokazu Sato – Gastroenterology

Press (with ugly title): The influence of fat when gut bacteria is reduced by antibioticsm – Science Daily

Animal microbiome

Harnessing the Microbiome to Prevent Fungal Infections: Lessons from Amphibians – Jenifer B. Walke – PLOS Pathogens

Built environment microbiome

Ten questions concerning the microbiomes of buildings – Rachel I. Adams – Building and Environment

The hot new 10 questions concerning the microbiomes of buildings will surprise you – Jonathan Eisen – MicroBEnet

Microbes in the news

“I’ll never let go, Jack I promise”
Titanic expected to disappear by 2030 thanks to hungry bacteria – Matthew Humphries – Geek.com
Video: Will Bacteria Completely Destroy The Titanic’s Remains? – MSN Video

Scientists find deadly scrub typhus bacteria in South America – Reuters

Mount Sinai Beth Israel Says Legionella Bacteria Found in Several Areas of Hospital – NY1.com

Mood, mind and memory: can gut bacteria meddle with the brain? – Dyani Lewis – Cosmos Magazine
Bugs as drugs – medicine’s next frontier – Dyani Lewis – Cosmos Magazine

Driving Microbiome Science: PKU and Probiotics – Raredr

Experts urge a defensive stance in efforts against antimicrobial resistance – EurekAlert

Microbes and money

Microban Opens Microbiology Testing Services to Non-Partners – Genevieve Scarano – Sourcing Journal

Science, publishing, and career

Your toughest experiment: taking the lead in the lab. Eight scientists share the secrets of being a successful PI – Times Higher Education

September 1, 2016

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Bedouins, urban Saoudis and monkeys, a subglacial lake, and the oldest microbial fossils.

Events

Alfred P. Sloan Foundation Workshop on Viruses to be Held in Singapore, January 2017 – David Coil – MicroBEnet

Human respiratory microbiome

News: Does barnyard dust protect Amish children from asthma? – Bryant Furlow – The Lancet

Human gut microbiome

Gut microbiome and dietary patterns in different Saudi populations and monkeys – Emmanouil Angelakis – Scientific Reports

Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Monika Fischer

Animal experiments

High fat diet drives obesity regardless the composition of gut microbiota in mice – Sylvie Rabot – Scientific Reports

Gut Microbiota Promote Angiotensin II–Induced Arterial Hypertension and Vascular Dysfunction – Susanne H. Karbach – Hypertension

Plant, root, and soil microbiome

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape – Rachel L. Vannette – Ecology

Review: Comparative phylogenomics of symbiotic associations – Pierre-Marc Delaux – New Phytologist

Water and extremophile

Microbial Community Structure of Subglacial Lake Whillans, West Antarctica – Amanda M. Achberger – Frontiers in Microbiology

Dust microbiome

Poultry houses: DNA from dust: comparative genomics of large DNA viruses in field surveillance samples – Utsav Pandey – bioRxiv

Techniques

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon – Riccardo Rosselli – Scientific Reports

More microbiology

Screen Shot 2016-09-01 at 06.30PM, Sep 01

Geological map and location of microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures – Allen P. Nutman – Nature

Press: Life thrived on young Earth: scientists discover 3.7-billion-year-old fossils – Science Daily
The World’s Oldest Fossils Are 3.7 Billion Years Old. The newly discovered rocks suggest that life arose very quickly after the Earth was formed – Ed Yong – The Atlantic

Microbes in the news

Microbial genomics and the future of food microbiology – Julie Wolf – American Society for Microbiology

Space Microbiome? Yes Please! and I’ll take a minION sequencer as well if you don’t mind – Ben Libberton – NPJ Biofilms Community

Multitalented microbiology student is highly lauded for her scholarship – Western Michigan University

Manuka honey makes bacteria less resistant to antibiotics – Rowena Jenkins – The Conversation

Changes in Gut microflora – early warning of Equine Metabolic Syndrome (EMS)? – Jackie Bellamy-Zions – Harness Link

uBiome Hires New Vice President of Research and Development: Dr. Audrey Goddard Joins from Genomic Health and Genentech – PR Web

Samorost 3’s fairy tale of microbiology is now on iPhone – Chris Priestman – Kill Screen

Science, publishing, and career

How to Motivate Your Employees: Give Them Compliments and Pizza – Melissa Dahl – New York Magazine

Opinion: Fixing Science’s Human Bias. It’s time to accelerate the conversation about why the research community is still not diverse – Edward Courchaine and Sarah Smaga – The Scientist

Thanks to the glass ceiling breakers – Yarrow Axford – Science

Peer review

HT: Tomer Altman: Stupid Patent of the Month: Elsevier Patents Online Peer Review – Electronic Frontier Foundation

Research Integrity

OMICS vs. The FTC: Plagiarism at a Predatory Publisher – Neuroskeptic – Discover