Category Archives: Human reproductive or urinary

March 10, 2017

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Ancient microbial DNA in Neanderthal dental calculus; the role of fungus in inflammatory bowel disease; symbiotic bacteria in the Hawaiian bobtail squid reproductive system; and a colorimetric/electrochemical device for detection of food and waterborne bacteria.

Events and jobs
Microbiology/Immunology Faculty – West Virginia School of Osteopathic Medicine – Lewisburg, West Virginia

Pregnancy and early life
Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota – Alyssa Robinson – Journal of Pediatric Gastroenterology and Nutrition

Review: Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – Mohan Pammi – Microbiome

Human oral microbiome
New approach for studying mobile genes using metagenomic analysis – K. Ishihara – Oral Diseases

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus – Laura S. Weyrich – Nature

In the News: Prehistoric ‘Aspirin’ Found in Sick Neanderthal’s Teeth – National Geographic

Human skin microbiome
Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool – Ning Chin – ProQuest Dissertations Publishing

Human vaginal microbiome
Review: The role of the vaginal microbiome in gynecological cancer: a review – Champer M. – BJOG

Human gut microbiome
A translational investigation into the role of dietary fatty acids in modulating endotoxemia and associated inflammation – Joshua Mark Lyte – ProQuest Dissertations Publishing

Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity – Malini Ahuja – Cell Metabolism

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – Herbert Tilg – Cell Metabolism

Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification – Shuang Jin – Scientific Reports

Gut microbiota modulation of chemotherapy efficacy and toxicity – James. L. Alexander – Nature Reviews Gastroenterology & Hepatology

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – Christian Barthels – Nature Communications

Faecal microbiota transplantation in clinical practice – E M Terveer – Gut

Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder – Ruth Ann Luna – Cellular and Molecular Gastroenterology and Hepatology
Animal experiments
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – Romeo Batacan – Journal of Applied Microbiology

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Chiaro TR – Science Translational Medicine

Animal microbiome
Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen – Henk J. Van Lingen – Frontiers in Microbiology

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome
Arsenic Transport in Rice and Biological Solutions to Reduce Arsenic Risk from Rice – Yanshan Chen – Frontiers in Plant Science

Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress – Shalaka Shinde – Frontiers in Plant Science

Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups – Jingjing Peng – Frontiers in Microbiology

Fertilization of Phaseolus vulgaris with the Tunisian rock phosphate affects richness and structure of rhizosphere bacterial communities – Darin Trabelsi – Applied Soil Ecology

Bioprospecting plant-associated microbiomes – Christina A. Muller – Journal of Biotechnology

Water and extremophile microbiome
Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation – MA Jebelli – Ecotoxicology and Environmental Safety

Performance and kinetics of membrane and hybrid moving bed biofilm-membrane bioreactors treating salinity wastewater – Alejandro Rodriguez-Sanchez – AlChE Journal

Metabolomics
Technological development of high-performance MALDI mass spectrometry imaging for the study of metabolic biology – Adam D. Feenstra – ProQuest Dissertations Publishing

Food microbiology
The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products – Solimar G. Machado – Frontiers in Microbiology

Culturable microorganisms during fermentation of Veltlínske zelené (Grüner Veltliner) ice wine – K. Ženišová – Journal of Food and Nutrition Research

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Probiotics/prebiotics
Case Study: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study – Elisa Salvetti – Applied Microbiology and Biotechnology

Techniques
Colorimetric and Electrochemical Bacteria Detection Using Printed Paper- and Transparency-Based Analytic Devices – Jaclyn A. Adkins – Analytical Chemistry

Microbes in the news
Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – The New York Times

Garrett’s non-microbiology picks
‘Plan bee’ drone artificially pollinates flowers on behalf of bees – Design Boom

March 9, 2017

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A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

March 7, 2017

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Events and jobs

Professor Of Microbiology – University of Western Australia – Last date: Friday, May 12, 2017

 

General microbiome

Biofilms: Microbial Cities Wherein Flow Shapes Competition – Su Chuen Chew – Trends in Microbiology

*Review: Critical Streptococcus suis Virulence Factors: Are They All Really Critical? – Mariela Segura – Trends in Microbiology

*Review: Collective Infectious Units in Viruses – Rafael Sanjuán – Trends in Microbiology

*Review: KSHV microRNAs: Tricks of the Devil – Jie Qin – Trends in Microbiology

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

 

Human oral microbiome

Chemotherapeutic decontamination of dental implants colonized by mature multispecies oral biofilm – Sebastien Dostie – Journal of Clinical Periodontology

 

Human vaginal microbiome

The presence of vaginal Lactobacillus species does not contribute to a measureable difference in amniotic fluid lactate levels collected from the vaginal tract of laboring women – Beverley Hall – AOGS

 

Animal microbiome

Effects of Pediococcus pentosaceus supplementation on growth performance, intestinal microflora and disease resistance of white shrimp, Litopenaeus vannamei – M. Adel – Aquaculture Nutrition

 

Plant, root and soil microbiome

Effects of the Inoculant Strain Pseudomonas sp. SPN31 nah + and of 2-Methylnaphthalene Contamination on the Rhizosphere and Endosphere Bacterial Communities of Halimione portulacoides – V Oliveira – Current Microbiology

Microbial-enhanced lindane removal by sugarcane (Saccharum officinarum) in doped soil-applications in phytoremediation and bioaugmentation. – J A Salam – Journal of Environmental Management

Immobilization remediation of Cd-polluted soil with different water condition – J Li – Journal of Environmental Management

Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat – Yudi M Lozano – New Phytologist

A long-term study of burning effects on a plant pathogen in tallgrass prairie – S. P. Dendy – Plant Pathology

 

Water and extremophile microbiome

Temperature–nutrient interactions exacerbate sensitivity to warming in phytoplankton – Mridul K. Thomas – Global Change Biology

 

Metagenomics and Bioinformatics

Omics for Understanding the Gut-Liver-Microbiome Axis and Precision Medicine – Jag Khalsa – Clinical Pharmacology in Drug Development

 

Techniques

Drug–Drug Interactions and Diagnostics for Drug Users With HIV and HIV/HCV Coinfections: Introduction – Jag H. Khalsa – Clinical Pharmacology in Drug Development

 

More Microbes

Influence of key physicochemical and hydrodynamic specifications of three packing materials on both performance and bacterial community structure of gas-biofilters – Luc Malhautier – Journal of Chemical Technology and Biotechnology

Metabolic coupling in bacteria – Shraddha Shitut – bioRxiv

Fungal derived 15-keto-prostaglandin E2 and host peroxisome proliferator-activated receptor gamma (PPAR-γ) promote C. neoformans growth during infection – Robert J Evans – bioRxiv

 

Microbes in news

Parkinson’s Linked to Changes in Gut Bacteria – T Pedersen – Psych Central

3.77 billion year old bacteria fossil may be Earth’s oldest, scientists say – J Leone – Journal-News

Bacterial vaginosis: A common health concern women must not take lightly – S Kantengwa – The New Times

This Drugstore Face Cream Is A Game Changer For People With Dry Skin – L Lebsack – Refinery29

UT researchers take new approach in cholera prevention – C Deangelis – The Blade

Bacteriophages Offer Potential for Helping Reduce Dependence on In-Feed Antibiotics – The Pig Site

Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – AE Carroll – The Upshot

Human Microbiome Market Worth 899.1 Million USD by 2025 – PRNewswire

Native Squid Used in Research of Environment and Human Health – Maui Now

March 5, 2017

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Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet.  Black carbon, one of the main components of air pollution,  is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival.  A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk.  And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Pregnancy and early life

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicenter inception cohort study – Subra Kugathasan – The Lancet

Multi-site human microbiome

Humans are colonized by many uncharacterized and highly divergent microbes -Mark A. Kowarsky -bioRxiv

Human respiratory microbiome

Air pollution alters Staphylococcus aureus and Streptococcus pneumonia biofilms, antibiotic tolerance and colonization – Shane J. K. Hussey – Journal of Environmental Microbiology

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.  

March 1, 2017

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Today’s digest features interesting reviews on the tole of gut microbiota in chronic kidney disease, and biotoxicity of soils from Mars. Impact of altered gut microbiota on bone strength in mice. Enjoy!

Events and jobs

Technical Service Representative (Microbiology) – ThermoFisher Scientific – Lenexa, Kansas

General microbiome

Review: Microbe social skill: the cell-to-cell communication between microorganisms – Xi Zhao – Science Bulletin

Review: Creating new business, economic growth and regional prosperity through microbiome-based products in the agriculture industry – Brajesh K. Singh – Microbial Biotechnology

Review: The link between inflammation, bugs, the intestine and the brain in alcohol dependence – S Leclercq – Translational Psychiatry

Editorial: The human microbiome: an emerging tool in forensics – Jarrad T. Hampton-Marcell – Microbial Biotechnology

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome – Ohad Manor – Cell Host and Microbe

Pregnancy and early life

Review: Transfer of maternal psychosocial stress to the fetus – Florian Rakers – Neuroscience & Biobehavioral Reviews

Vaginal microbiome

Survival of vaginal microorganisms in three commercially available transport systems – Allison L. DeMarco – Anaerobe

Human skin microbiome

Review: Towards personalized modification of microbial imbalances – J.E.E. Totté – British Journal of Dermatology

Human gut microbiome

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

*Review: Gut microbiota in chronic kidney disease – Secundino Cigarran Guldris – Nefrología (English Edition)

Review: The clinical value of breath hydrogen testing – Chu K Yao – Journal of Gastroenterology and Hepatology

Commentary: Atopic dermatitis and gut microbiota – M. Lindberg – British Journal of Dermatology

Animal experiments

SYN-004 (ribaxamase), an Oral Beta-Lactamase, Mitigates Antibiotic-Mediated Dysbiosis in a Porcine Gut Microbiome Model – Sheila Connelly – Journal of Applied Microbiology

*Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Plant, root, and soil microbiome

*Biotoxicity of Mars Soils: 2. Survival of Bacillus subtilis and Enterococcus faecalis in Aqueous Extracts Derived from Six Mars Analog Soils – Andrew C. Schuerger – Icarus

Food microbiology

Polyphenolic extracts of cherry (Prunus cerasus L.) and blackcurrant (Ribes nigrum L.) leaves as natural preservatives in meat products – Agnieszka Nowak – Food Microbiology

Probiotics / prebiotics

Effects of synbiotic supplementation on growth performance, carcass characteristics, meat quality and muscular antioxidant capacity and mineral contents in broilers – Yefei Cheng – Journal of the Science of Food and Agriculture

GH11 xylanase increases prebiotic oligosaccharides from wheat bran favouring butyrate-producing bacteria in vitro – Jonas Laukkonen Ravn – Animal Feed Science and Technology

Effects of Bacillus subtilis strains and the prebiotic Previda® on growth, immune parameters and susceptibility to Aeromonas hydrophila infection in Nile tilapia, Oreochromis niloticus – Samuel Addo – Aquaculture Research

Enhancing growth and resistance to Vibrio alginolyticus disease in catarina scallop (Argopecten ventricosus) with Bacillus and Lactobacillus probiotic strains during early development – Fernando Abasolo-Pacheco – Aquaculture Research

The association of a probiotic with a prebiotic (Flortec, Bracco) to improve the quality/quantity of spermatozoa in infertile patients with idiopathic oligoasthenoteratospermia: a pilot study – C. Maretti – Andrology

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – Dong Ji-lin – Journal of the Science of Food and Agriculture

Microbes in the news 

WHO: These 12 bacteria pose greatest risk to human health

A Bizarre Bacteria Could Be the Key to Controlling Mosquitoes

Flesh-eating bugs lurking on ATMs and killer bacteria found on phones

Microbes on the market 

Proof-of-Concept Study Published in Clinical Microbiology and Infection Reports the Benefit of PathoQuest NGS-Based Metagenomics Test to Identify Clinically-Relevant Pathogens in Immunocompromised Patients Suspected of Infection

Anitha’s non-microbiology picks

Glass Microbiology at the At-Bristol Science Centre

Mysterious ‘Cosmic’ Jellyfish Spotted in Remote Ocean Depths

Unity Biotechnology: Investment In A Long And Healthy Life Becoming Possible

February 27, 2017

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The ‘horseshoe effect’ in analyzing microbial niches; fecal microbiota transplantation (FMT) in immunocompromised individuals; effects of long-term ceftriaxone sodium administration on gut microbiota diversity; DNA extraction bias in soil microbial community analysis; and a multistrain probiotic clinical trial in NAFLD.

Events and jobs

Postdoctoral Fellow in Microbiology – University of Tennessee Health Science Center, Memphis, TN

QC Microbiology Analyst – Leidos – Frederick, MD

General microbiome
Uncovering the Horseshoe Effect in Microbial Analyses – James T. Morton – mSystems

Pregnancy and early life
Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Implications of intrapartum azithromycin on neonatal microbiota – Jenny Mei – The Lancet Infectious Diseases

Human respiratory microbiome
Restoring CFTR Function Reduces Airway Bacteria and Inflammation in People With Cystic Fibrosis and Chronic Lung Infections – Katherine B. Hisert – American Journal of Respiratory and Critical Care Medicine

Microbiome of the Lung in Patient with Idiopathic Pneumonia Syndrome (IPS) after HCT – Sachiko Seo – Biology of Blood and Marrow Transplantation

Oral and nasal microbiota in Parkinson’s disease – Pedro A.B. Pereira – Parkinsonism & Related Disorders

Human skin microbiome
N-acetylcysteine inhibits growth, adhesion and biofilm formation of Gram-positive skin pathogens – Daria Eroshenko – Microbial Pathogenesis

Human vaginal microbiome
Olegusella massiliensis gen. nov., sp. nov., strain KHD7T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis – Khoudia Diop – Anaerobe

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobe

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women – Vodstrcil LA – PLoS One

Human gut microbiome
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system – Yanjie Guo – Scientific Reports

Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota – Danielle N. Cooper – Nutrients

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Gut microbiota and systemic inflammation changes after bread consumption: The ingredients and the processing influence – Maykel Arias – Journal of Functional Foods

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wong – Microbial Pathogenesis

The dual role of short fatty acid chains in the pathogenesis of autoimmune disease models – Mizuno M – PLoS One

Giardia duodenalis induces dysbiosis of human intestinal microbiota biofilms – Jennifer K. Beatty – International Journal for Parasitology

Animal experiments
Apple Polysaccharide inhibits microbial dysbiosis and chronic inflammation and modulates gut permeability in HFD-fed rats – Sheng Wang – International Journal of Biological Macromolecules

Animal microbiome
Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle – Fuyong Li – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Review: Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding – Samuel Kroll – Current Opinion in Plant Biology

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬ – Ines Aline Aschenbrenner – Molecular Ecology

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils – Adrienne B. Narrowe – Environmental Microbiology

A comprehensive phylogenetic analysis of copper transporting P1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes – Ciro Cubillas – Microbiology Open

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Loss of soil microbial diversity may increase insecticide uptake by crop – Min Zhang – Agriculture, Ecosystems & Environment

The presence of aggressive ants is associated with insect visits to coffee flowers and floral microbe communities – Rachel L. Vannette – Basic and Applied Ecology

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy – P. Bhattacharyya – Science of the Total Environment

The Introduction of Woody Plants For Freshwater Wetland Restoration Alters The Archaeal Community Structure in Soil – Xiao-Yan Liu – Land Degradation & Development

A distinctive root-inhabiting denitrifying community with high N2O/(N2O+N2) product ratio – Chao Ai – Soil Biology and Biochemistry

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Water and extremophile microbiome
Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds – Jingjing Wang – International Aquatic Research

Serpentinization-influenced groundwater harbors extremely low diversity microbial communities adapted to high pH – Katrina I. Twing – Frontiers in Microbiology

Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi – Timothy J. Williams – Environmental Microbiology

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of the Total Environment

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters – Carmen Falagán – Extremophiles

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms – Timothy Sibanda – Microbial Biotechnology

Acinetobacter halotolerans sp. nov., a novel halotolerant, alkalitolerant, and hydrocarbon degrading bacterium, isolated from soil – Ram Hari Dahal – Arhives of Microbiology

Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature – Robert Ccorahua-Santo – Research in Microbiology

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – Microbiology Open

Food microbiology
Nondairy beverage produced by controlled fermentation with potential probiotic starter cultures of lactic acid bacteria and yeast – Ana Luiza Freire – International Journal of Food Microbiology

Probiotics / prebiotics
Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice – Aurelijus Burokas – Biological Psychiatry

Review: Clinical effects of probiotics in cystic fibrosis patients: A systematic review – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Effects of Multistrain Probiotic Supplementation on Glycemic and Inflammatory Indices in Patients with Nonalcoholic Fatty Liver Disease: A Double-Blind Randomized Clinical Trial – Abbaszadeh Sepideh – Journal of the American College of Nutrition

Microbes in the news
Glass Microbiology at the At-Bristol Science Centre – Culture Calling

Bacteria And Babies: A Scientific Debate – Part One – American Council on Science and Health

Reference: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns – Maria G. Dominguez-Bello – PNAS

February 23, 2017

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Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 17, 2017

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Today the incoming is filled with some compelling reviews; considering periodontal inflammation and C.diff with IBD (separately), as well some biopesticide ethics discussion, and mention of exciting biome research mergers and funding afoot. Read on!

Human oral microbiome

Review: Contribution of proteomics to our understanding of periodontal inflammation– Nagihan Bostanci- Proteomics

Human vaginal microbiome

Subclinical alteration of the cervical–vaginal microbiome in women with idiopathic infertility-Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Review: Systematic review with meta-analysis: the impact of Clostridium difficile infection on the short and long-term risks of colectomy in inflammatory bowel disease– Law C- Alimentary Pharmacology and Therapeutics

Review: Therapeutic modulation of gut microbiota in inflammatory bowel disease: More questions to be answered– Yu Qi Qiao- Journal of Digestive Diseases

Fecal microbiota

Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study– Christopher Staley- The American Journal of Gastroenterology

Plant, root, and soil microbiome

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes– Gomba A.- Journal of Applied Microbiology

Biopesticides

Review: Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?– Caroline Pandin- Microbial Biotechnology
http://onlinelibrary.wiley.com/doi/10.1111/1751-7915.12693/full

Microbes in the news

Laundry hygiene—how to get more than clean- Bockmuhl DP- Applied Microbiology

DNA Analysis Reveals Secret Microbiomes in Cities– Paula Solferini Rothman- BU News Service

Microbes on the market

Symbiotix Biotherapies Announces Issuance of First Composition of Matter Patent Covering a Microbiome-derived Therapeutic Molecule– Yahoo Finance

Vedanta Teams with Stanford and Leiden Universities for Microbiome Therapeutics– Genetic Engineering and Biotechnology News

Research Funding

U Of M Commercialization Grants Target Microbiome Test, Sleep Disorders, Epilepsy- Dan Jacobson– Twin Cities Business

February 17, 2017

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Today the incoming research is rich in reviews, including one article examining periodontal inflammation and another examining  C.diff and IBD, also a biopesticide ethics discussion and some exciting funding and research mergers in the mix. Read on!

Human oral microbiome

Review: Contribution of proteomics to our understanding of periodontal inflammation– Nagihan Bostanci- Proteomics

Human vaginal microbiome

Subclinical alteration of the cervical–vaginal microbiome in women with idiopathic infertility-Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Review: Systematic review with meta-analysis: the impact of Clostridium difficile infection on the short and long-term risks of colectomy in inflammatory bowel disease– Law C- Alimentary Pharmacology and Therapeutics

Review: Therapeutic modulation of gut microbiota in inflammatory bowel disease: More questions to be answered– Yu Qi Qiao- Journal of Digestive Diseases

Fecal microbiota

Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study– Christopher Staley- The American Journal of Gastroenterology

Plant, root, and soil microbiome

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes– Gomba A.- Journal of Applied Microbiology

Biopesticides

Review: Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?– Caroline Pandin- Microbial Biotechnology

Microbes in the news

Review: Laundry hygiene—how to get more than clean– Bockmuhl DP- Applied Microbiology

DNA Analysis Reveals Secret Microbiomes in Cities– Paula Solferini Rothman- BU News Service

Vedanta Teams with Stanford and Leiden Universities for Microbiome Therapeutics– Genetic Engineering and Biotechnology News

Microbes on the market

Symbiotix Biotherapies Announces Issuance of First Composition of Matter Patent Covering a Microbiome-derived Therapeutic Molecule- Yahoo Finance

Research Funding

U Of M Commercialization Grants Target Microbiome Test, Sleep Disorders, Epilepsy- Dan Jacobson– Twin Cities Business

February 16, 2017

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Events and jobs

 Microbiology assistant or associate professor – Universidad de los Andes (Bogotá, Colombia)

PhD – Mechanisms of bacterial community dynamics in oral biofilms – The University of Sheffield, UK

General microbiome

Microbiome and Cardiac Health – Enrico Biffi – Integrative Cardiology

Editorial: Signals to sociality: how microbial communication fashions communities – Karine A. Gibbs – FEMS Microbiology Reviews

Pregnancy and early life

Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial – Wafaa Qasem – BMC Pediatrics

Human oral microbiome

Dysbiosis of oral buccal mucosa microbiota in patients with oral lichen planus – Yuan He – Oral Diseases

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis – Dongmei Ai – BMC Genomics 2017

Human respiratory microbiome

Bacterial Topography of the Healthy Human Lower Respiratory Tract – Robert P. Dickson – American Society for Microbiology (mBio)

Human vaginal microbiome

Distinct effects of the cervico-vaginal microbiota and herpes simplex type 2 infection on female genital tract immunology – Shannon B. – The Journal of Infectious Diseases

Human gut microbiome

DIFFERENCES IN GUT MICROBIOTA ACTIVITY (ANTIMICROBIALS, POTENTIAL MUTAGENS, AND STEROLS) ACCORDING TO DIET – P. OLEJNÍKOVÁ – Acta Alimentaria

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leeuwenhoek

Diversity and enterotype in gut bacterial community of adults in Taiwan – Chao Liang – BMC Genomics

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn’s disease in the Ryukyu Islands – Shigeki Nakagome – Human Genetics

Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention – Guojun Wu – American Socieity for Microbiology (mBio)

Review: Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases – Lieke WJ van den Elsen – Clinical and Translational Immunology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes – Julia H. Kreznar – Cell Reports

Melatonin prevents obesity through modulation of gut microbiota in mice – Pengfei Xu – Journal of Pineal Research

Inonotus obliquus polysaccharide regulates gut microbiota of chronic pancreatitis in mice – Yang Hu – AMB Express

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet – Sophie Comtet-Marre – Frontiers in Microbiology

Animal microbiome

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island – Jan M. Meyer – Environmental Microbiology

Plant, root, and soil microbiome

Effect of Elevated UV-B Radiation on Microbial Biomass C and Soil Respiration in Different Barley Cultivars Under Field Conditions – Yunsheng Lou – Water, Air, Soil Pollution

Comment: Isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of Maize seedlings in greenhouses – Jeffrey S. Norman – Frontiers in Plant Science

Effects of Vegetation and Temperature on Nutrient Removal and Microbiology in Horizontal Subsurface Flow Constructed Wetlands for Treatment of Domestic Sewage – Qingwei Zhou – Water, Air, Soil Pollution

Editorial: Biotrophic Plant-Microbe Interactions – Pietro D. Spanu – Frontiers in Plant Science

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA – Kathleen H. Lavoie – PloS ONE

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community – Lu Shi – Scientific Reports

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank – Marcio F. A. Leite – Scientific Reports

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil – Pengfei Liu – Environmental Microbiology

Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles – C. F. McGee – Ecotoxicology

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system – Jun Zhao – Environmental biotechnology

Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil – Manli Wu – Environmental Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems – Celine Pisapia – Frontiers in Microbiology

Food microbiology

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases – David F. Nieuwenhuijse – Frontiers in Microbiology

Masters Thesis: Effects of Cavitation on the Removal and Inactivation of Listeria and Salmonella from the Surface of Tomatoes and Cantaloupe – Joshua Jungho Lee – Virginia Tech

Chemical characterization of the glycated myofibrillar proteins from grass carp (Ctenopharyngodon idella) and their impacts on the human gut microbiota in vitro fermentation – Kaining Han – Food & Function

Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination – Etienne V. Doll – Frontiers in Microbiology

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products – Aoife J. McHugh – Frontiers in Microbiology

Probiotics / prebiotics

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota – V.D.V. Valeriano – Journal of Applied Microbiology

Physiological Changes of Surface Membrane in Lactobacillus with Prebiotics – Mingfang Pan – Journal of Food Science

Bioinformatics

Comparative Analysis of Soil Microbiome Diversity using QIIME and CloVR Pipelines – Puniethaa Prabhu – Biometrics and Bioinformatics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman (Duke University) – eLife

MetaTopics: an integration tool to analyze microbial community profile by topic model – Jifang Yan – BMC Genomics 2017

Enhancing the clinical coverage and anticancer efficacy of immune checkpoint blockade through manipulation of the gut microbiota – Jonathon M. Pitt – OncoImmunology

Techniques         

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research – Sebastian Menke – Frontiers in Microbiology

Microbes on the market 

Day Two link with Johnson & Johnson on personalized microbiome analysis for diabetes nutrition – Eliot Beer – nutraingredients.com

Microbes in the news

News Feature: Cleaning up the hygiene hypothesis – Megan Scudellari – PNAS

Ed’s non-microbiology picks

Decline in global oceanic oxygen content during the past five decades – Sunke Schmidtko – Nature

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum – Christian Kehlmaier – Proceedings of the Royal Society (Biological Sciences)

Long-term trends in the honeybee ‘whooping signal’ revealed by automated detection – Michael Ramsey – PloS One