Category Archives: Food Microbiology

December 10, 2016

Posted on by

Airway microbiota of infants with cystic fibrosis, an X-linked IBD risk gene in mice, Colorado flood impact, and metabolic profiling of men eating pasta and bread.

General microbiome

Review: Arguments Reinforcing the Three-Domain View of Diversified Cellular LifeArguments Reinforcing the Three-Domain View of Diversified Cellular Life – Arshan Nasir – Archaea

Opinion: Koch’s Postulates to Metagenome and NextGeneration Sequencing, But what is Next? – Santanu Chattopadhyay – Journal of Gastrointestinal Disorders and Liver Function

Human oral microbiome

Review: Gram-Positive Anaerobes in Periodontal Pathogenesis: New Kids on the Block? – A Mini Review – Journal of Bacteriology & Mycology:

Human respiratory microbiome

* Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis – Theresa A. Laguna – PLOS ONE

The Microbiome and the Pathophysiology of Asthma – Ashley Sullivan – Respiratory Research

Human gut microbiome

Review: Intestinal Immunity and Gut Microbiota in Atherogenesis – Tomoya Yamashita – Journal of Atherosclerosis and Thrombosis

Review: Microbiome, Growth Retardation, and Metabolism: Are they related? – Daniel J. Hoffman – Annals of Human Biology

Animal experiments

Cosmc is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk – Matthew R. Kudelka – PNAS

Depletion of Gut Microbiota Protects against Renal Ischemia-Reperfusion Injury – Diba Emal – Journal of the American Society of Nephrology

Probiotic Roles of Lactobacillus spp. in Swine: Insights from Gut Microbiota – Valerie Diane V. Valeriano – Journal of Applied Microbiology

Gut microbiota from metabolic disease-resistant, macrophage-specific RIP140 knockdown mice improves metabolic phenotype and gastrointestinal integrity – Yi-Wei Lin – Scientific Reports

Antimicrobial growth promoters modulate host responses in mice with a defined intestinal microbiota – Kirsty Brown – Scientific Reports

High Fibre Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in DOCA-Salt Hypertensive Mice
Francine Z. Marques – Circulation

Plant, root, and soil microbiome

Microbial remediation of aromatics-contaminated soil – Ying Xu – Frontiers of Environmental Science & Engineering

Plant pathogens but not antagonists change in soil fungal communities across a land abandonment gradient in a Mediterranean landscape – L. Bosso – Acta Oecologica

High taxonomic variability despite stable functional structure across microbial communities – Stilianos Louca – Nature Ecology & Evolution

Repeated glyphosate exposure induces shifts in nitrifying communities and metabolism of phenylpropanoids – Marco Allegrini – Soil Biology and Biochemistry

Water microbiology

Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea – Kai Wang – Scientific Reports

Influence of the Po River runoff on the bacterioplankton community along trophic and salinity gradients in the Northern Adriatic Sea – Ilaria Pizzetti – Marine Ecology

Dynamic metabolic exchange governs a marine algal-bacterial interaction – Einat Segev – eLIFE
Research highlight: When a relationship turns ugly – Andrea Du Toit – Nature Reviews Microbiology

Food microbiology and functional foods

Cultivable microbiome of fresh white button mushrooms – Werner Rossouw

A MeSH-based text mining method for identifying novel prebiotics – Shan, Guangy – Medicine

Waste and pollution microbiology

Effect of structural carbohydrates and lignin content on the anaerobic digestion of paper and paper board materials by anaerobic granular sludge – Jorge Gonzalez-Estrella – Biotechnology and Bioengineering

* Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes – Emily Garner – Scientific Reports

Sequential bioleaching of copper from brake pads residues using encapsulated bacteria – François Vermeulen – Minerals Engineering

Feed it some of your old protein gels: Isolation and Characterization of Acrylamidase from Arthrobacter sp. DBV1 and Its Ability to Biodegrade Acrylamide – Dattatray K. Bedade – Applied Biochemistry and Biotechnology

Copper exposure to soil under single and repeated application: Selection for the microbial community tolerance and effects on the dissipation of antibiotics – Bei Liu – Journal of Hazardous Materials

Resistome

A diverse intrinsic antibiotic resistome from a cave bacterium – Andrew C. Pawlowski – Nature Communications

Million-Year-Old ‘Hero Bug’ Emerges From Cave – Michaeleen Doucleff – NPR

Metabolomics

* Metabolic Profiling Reveals Differences in Plasma Concentrations of Arabinose and Xylose after Consumption of Fiber-Rich Pasta and Wheat Bread with Differential Rates of Systemic Appearance of Exogenous Glucose in Healthy Men – Andre J Pantophlet – The Journal of Nutrition

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways – Kieran James – Scientific Reports

Viruses and phages

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses – Simon Roux – PeerJ

Microbial ecology

Paradoxes in Leaky Microbial Trade – Yoav Kallus – bioRxiv

Microbes in the news

Video: Living together: the symbiosis of host-microbial interactionsVideo: Living together: the symbiosis of host-microbial interactions – Margaret McFall-Ngai – iBiology

Scientist Studies the Infant Resistome to Combat Superbugs – Infection Control Today

Diet, the gut microbiome, and colorectal cancer: are they linked? – EurekAlert

 

Microbes on the market

Medical Game-Changers Beckon. On #1 of the Top 10: Using the Microbiome to Prevent, Diagnose, and Treat Disease –  Casey McDonald

VC-backed Enterome hires Patel as chief medical officer and adds Garceau to board – PE Hub

Second Genome Announces Appointments in Human Resources, Finance to Support Corporate Growth – Yahoo.com

As school gardens spread, so do the teaching moments – Adrian Higgins – Washington Post

Twitter as a Tool for Teaching and Communicating Microbiology: The #microMOOCSEM Initiative – EHU

New evidence shows how bacterium in undercooked chicken causes GBS – EurekAlert

Science, publishing, and career

The Microbiology Effect: A Call for Education Research – Samantha L. Elliott – J. Microbiol. Biol. Educ.
The Necessity of Prerequisite Undergraduate Microbiology Courses for Pre-Allied Health Professionals – Andrea M. Rediske – J. Microbiol. Biol. Educ.
Supporting Microbiology in the Nursing Curriculum – Bethany Adamec – ASM

On the origin of nonequivalent states: how we can talk about preprints – Cameron Neylon – bioRxiv

Why a First Amendment win is good for science – Adam Marcus and Ivan Oransky – STATNews

December 9, 2016

Posted on by

Human oral microbiome

Chapter Four – The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases – B. Sampaio-Maia – Advances in Applied Microbiology

Protocol: Methods to Study Antagonistic Activities Among Oral Bacteria – Fengxia Qi – Oral Biology

Protocol: The Oral Microbiota in Health and Disease: An Overview of Molecular Findings – José F. Siqueira Jr. – Oral Biology

Human skin microbiome

The protective effect of microbiota on S. aureus skin colonization depends on the integrity of the epithelial barrier – Marc Burian – Journal of Investigative Dermatology

Human respiratory microbiome (also Early Life)

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy – Christian Rosas-Salazar – The Journal of Infectious Diseases

Reemergence of Lower-Airway Microbiota in Lung Transplant Patients with Cystic Fibrosis – Saad A. Syed – Annals of the American Thoracic Society

Editorial: Changes in the Cystic Fibrosis Airway Microbiome after Lung Transplant: The More Things Change, the More They Stay the Same – Shawn D. Aaron – Annals of the American Thoracic Society

Human gut microbiome

Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia – Guillaume A. Durand – Anaerobe

Review: Formation of propionate and butyrate by the human colonic microbiota – Petra Louis – Environmental Microbiology

Review: Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes – Allison Clark – Journal of the International Society of Sports Nutrition

Animal experiments

Analysis of the intestinal microbial community and inferred functional capacities during the host response to Pneumocystis pneumonia – Derrick R. Samuelson – Experimental Lung Research

Plant, root, and soil microbiome

The prey’s scent – Volatile organic compound mediated interactions between soil bacteria and their protist predators – Kristin Schulz-Bohm – The ISME Journal

How miniature predators get their favorite soil bacteria. Sniffing out your dinner in the dark – Science Daily

Food microbiology

Dynamics of microbial community during the extremely long-term fermentation process of a traditional soy sauce – Yang Yang – Journal of the Science of Food and Agriculture

Water microbiology

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors – Minghong Gao – Microbial Ecology

Phages and viruses

Exploring the contribution of bacteriophages to antibiotic resistance – Itziar Lekunberri – Environmental Pollution

Bioinformatics and metagenomics

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries – Kamlesh Jangid – PLOS ONE

More microbiology

17th Century Variola Virus Reveals the Recent History of Smallpox – Ana T. Duggan – Current Biology

A Mummy’s DNA May Help Solve The Mystery Of The Origins Of Smallpox – Nell Greenfieldboyce – NPR

Drug resistant pathogens and travel: No road map but a new initiative from Travel Medicine and Infectious Disease – Patricia Schlagenhauf – Travel Medicine and Infectious Disease

Microbes in the news

uBiome Joins Google, SpaceX, and Oculus as 2016 World Technology Award Finalist – PR Web

Paul Schreckenberger, microbiology lab director at Loyola, dies at 69 – Chicago Tribune

Antibacterial products may help bacteria beat antibiotics – Bob Holmes

Corticosteroid Success Linked to Differences in Bronchial Microbiome – Kenneth Bender – HCP live

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences — Part IX, The Microbiome and Immunotherapy II – David Puelo – JDSupra

Scientist Studies the Infant Resistome to Combat Superbugs – Infection Control Today

The Microbiome and Risk for HIV: Research in South Africa shows how the balance of bacteria in a woman’s vagina can raise or lower her risk for HIV – Columbia

December 3, 2016, part 2

Posted on by

Recognition of extremophilic archaeal viruses by eukaryotic cells, special issue about the holobiont concept, sleep deprivation, respiratory viruses in infants. So many new papers that I had to spend another couple of hours on the digest today!

General microbiome and ecology

* Themed issue with papers about the holobiont and endosymbionts: Biological Individuality – Biology & Philosphophy

Review: Making a microbiome: the many determinants of host-associated microbial community composition – Karen L Adair – Current Opinion in Microbiology

Pregnancy and early life

* Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants – Insa Korten – mSphere

Does vaginal delivery mitigate or strengthen the intergenerational association of overweight and obesity? Findings from the boston birth cohort – N T Mueller – International Journal of Obesity

The oral cavities of healthy infants harbor high proportions of Streptococcus salivarius strains with phenotypic and genotypic resistance to multiple classes of antibiotics – Thaís H. Palma – Journal of Medical Microbiology

Human respiratory microbiome

Bacterial community collapse: A meta-analysis of the sinonasal microbiota in chronic rhinosinusitis – Brett Wagner Mackenzie – Environmental Microbiology

Review: Viral-Bacterial interactions in the respiratory tract – Carla Bellinghausen – Journal of General Virology

Human skin microbiome

Dysbiotic Bacterial and Fungal Communities Not Restricted to Clinically Affected Skin Sites in Dandruff – Renan C. Soares – Frontiers in Cellular and Infection Microbiology

Gene Function Analysis in the Ubiquitous Human Commensal and Pathogen Malassezia Genus – Giuseppe Ianiri – mBio

Review: Microbial biofilms and the human skin microbiome – Michael Brandwein – NPJ Biofilms and Microbiomes

Human gut microbiome

Clostridium difficile carriage in adult cystic fibrosis (CF); implications for patients with CF and the potential for transmission of nosocomial infection – D.G. Burke – Journal of Cystic Fibrosis

* Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals – Christian Benedict – Molecular Metabolism

Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients – Xiao Wei – Frontiers in Microbiology

Review: Role of gut microbiota in atherosclerosis – Annika Lindskog Jonsson- Nature Reviews Cardiology

Review: The role of diet on gut microbiota composition – S. Bibbò – European Review for Medical and Pharmacological Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes – Elizabeth L. Johnson – Journal of Molecular Medicine

Review: Gut Homeostasis, Microbial Dysbiosis, and Opioids – Fuyuan Wang – Toxicologic Pathology

Animal and in vitro experiments

Sensitive and Simplified Detection of Antibiotic Influence on the Dynamic and Versatile Changes of Fecal Short-Chain Fatty Acids – Xiaoya Zhao – PLOS ONE

* Recognition of extremophilic archaeal viruses by eukaryotic cells: a promising nanoplatform from the third domain of life – Kristine Buch Uldahl – Scientific Reports

Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk – Kalaimathi Govindarajan – PLOS ONE

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs – Anne-Lie Blomström – PLOS ONE

Intraluminal Flagellin Differentially Contributes to Gut Dysbiosis and Systemic Inflammation following Burn Injury – Logan Grimes – PLOS ONE

Early-Life Sugar Consumption Affects the Rat Microbiome Independently of Obesity –
Emily E Noble – Journal of Nutrition

Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Dietary fat and gut microbiota interactions determine diet-induced obesity in mice – Raphaela Kübeck – Molecular Metabolism

Animal microbiome

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment –
Christine V. Avena – Frontiers in Microbiology

Plant, root, and soil microbiome

A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes – Vilma Ortiz – BMC Ecology

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China – Min Liu – Canadian Journal of Microbiology

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach – Véronique Gourmelon – PLOS ONE

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain – Min Jung Kwon – Global Change Biology

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China – Zhi-Feng Zhou – Archives of Environmental Contamination and Toxicology

Method: Assessing Bacterial and Fungal Diversity in the Plant Endosphere – Bernd Wemheuer – Methods in Molecular Biology: Metagenomics

Water microbiome

Method: Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies – Dominik Schneider – Methods in Molecular Biology: Metagenomics

Method: Construction and Screening of Marine Metagenomic Large Insert Libraries – Nancy Weiland-Bräuer – Methods in Molecular Biology: Metagenomics

Food microbiology

Microbiological Quality and Variability of Natural Microbiota in Croatian Cheese Maturing in Lambskin Sacks – Jadranka Frece – Food Technology and Biotechnology

Bioinformatics and metagenomics

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing – Hardik I. Parikh – BMC Bioinformatics

Microbes in the news

Podcast (17 min) – Tracking the Daily Rhythms of the Microbiome – Science Friday

ASM delivers “Gift of Knowledge” to Ethiopia with Microbiology Mentoring Program – ASM

Science, publishing, and career
How Trump Could Wage a War on Scientific Expertise. The mechanics of stripping empiricism out of America’s regulatory systems – Ed Yong – The Atlantic

November 29, 2016

Posted on by

Metabolic reconstruction for 773 gut microbes, host genetics vs diet in the mouse gut, microbiology of a range of food items, and citizen scientists collecting arthropods (let’s call that microbiology today; I’m feeling generous).

Human gut microbiome
* Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota – Stefanía Magnúsdóttir – Nature Biotechnology

Animal models

* Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome – Antoine M. Snijders – Nature Microbiology

Genes, early environment sculpt the gut microbiome – EurekAlert

Animal microbiome

Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects – Gustavo Vasconcelos Bastos Paulino – Marine Pollution Bulletin

Plant, root, and soil microbiology

Bacterial diversity patterns differed in two developing ecosystems – Shankar G. Shanmugam – Microbial Ecology

Identifying the microbial taxa that consistently respond to soil warming across time and space – Angela M. Oliverio – Global Change Biology

Food microbiology

Exploring the microbiota of the red-brown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems – Raffaele Guzzon – Food Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota – Lin-Huan Wu – Food Microbiology

Monitoring of wheat lactic acid bacteria from the field until the first step of dough fermentation – Antonio Alfonzo – Food Microbiology

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef – Elina Säde – Food Microbiology

Characterization of the microbiota in lightly salted bighead carp (Aristichthys nobilis) fillets stored at 4 °C – Xiaochang Liu – Food Microbiology

More microbiology

An essential role for bacterial nitric oxide synthase in Staphylococcus aureus electron transfer and colonization – Traci L. Kinkel – Nature Microbiology

Staph uses nitric oxide enzyme to colonize noses – Phys.org

Microbes in the news

Gift Guide for the Grown Ups On Your List. #10. Sequence the bacteria in your gut! – Mrs Ice Cream – Hellobee

Microbiome & Nutrigenomic Medicine Seminar: Cybermonday special – gifts for you  – upcoming The Gut Institute Event in Berkeley, 10/11 December– Dr. Grace – YouTube

Microbiology in a brewery! – MicroHoldingScience

Qiagen and CosmosID launch metagenomics analysis plugin – Joe Whitworth – Food Quality News

China’s Smog Could Make It More Difficult To Fight Off Some Infections. The air pollution in Beijing has traces of antibiotic-resistant bacteria – Lindsey Pulse – Newsy.com

Bik’s Non-Microbiology Picks

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses – Anne A. Madden – Molecular Ecology

Study Highlights Diversity of Arthropods Found in Homes Across the United States – From Swabs of Dust – NC State University

November 28, 2016

Posted on by

Chronic rhinosinusitis, quantification of vaginal lactobacilli, intestinal nitrogen constraints, the eelgrass microbiome, microbes under lake ice.

Human respiratory microbiome

* Classification of Chronic Rhinosinusitis—Working Toward Personalized Diagnosis – Adam S. DeConde – Otolaryngologic Clinics of North America
Bacterial Pathogens and the Microbiome – Thad W. Vickery – Otolaryngologic Clinics of North America

 
Human skin microbiome

Comment on “Skin Microbiome Surveys Are Strongly Influenced by Experimental Design” – Patrick L.J.M. Zeeuwen – Journal of Investigative Dermatology

Establishing Tolerance to Commensal Skin Bacteria: Timing Is Everything – Tiffany C. Scharschmidt – Dermatologic Clinics

Human vaginal microbiome

* A novel real-time PCR assay for highly specific detection and quantification of vaginal lactobacilli – Vladimir V. Demkin – Molecular and Cellular Probes

Human gut microbiome

Review: Interaction of gut microbiota with bile acid metabolism and its influence on disease states – Christopher Staley – Applied Microbiology and Biotechnology

Review: Microbes Dress for Success: Tolerance or Resistance? – Janelle S. Ayres – Trends in Microbiology

* Review: Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints – Andrew J. Holmes – Cell Metabolism

Animal models

The gut microbiota in young and middle-aged rats showed different responses to chicken protein in their diet – Yingying Zhu – BMC Microbiology

The Drosophila transcriptional network is structured by microbiota – Adam J. Dobson – BMC Genomics

Review: Norovirus Regulation by Host and Microbe – Megan T. Baldridge – Trends in Molecular Medicine

Plant, root, and soil microbiome

* Global-scale structure of the eelgrass microbiome – Ashkaan K Fahimipour – bioRxiv

Rapid bacteria identification from environmental mining samples using MALDI-TOF MS analysis – Ingrid Regina Avanzi – Environmental Science and Pollution Research

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches – Shin Ae Lee – Journal of Microbiology

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea – Jeong Myeong Kim – Journal of Microbiology

Chemical, organic and bio-fertilizer management practices effect on soil physicochemical property and antagonistic bacteria abundance of a cotton field: Implications for soil biological quality – Rui Li – Soil and Tillage Research

Water and extremophile microbiome

* Ecology under lake ice – Stephanie E. Hampton – Ecology Letters

Food microbiology

Dynamics of bacterial communities during manufacture and ripening of traditional Caciocavallo of Castelfranco cheese in relation to cows’ feeding – Marina Giello – Food Microbiology

Metagenomics and bioinformatics

MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles – Grace Tzun-Wen Shaw – BMC Bioinformatics

Metabolomics

Metabolomic profile of children with recurrent respiratory infections – Sara Bozzetto – Pharmacological Research

Microbes in the news

Infant Microbiome: Vaginal Delivery Versus C-Section – Jef Akst – The Scientist

I did not get the first part of this title. Michael Pollan didn’t invent microbiome research, he’s a demagogue: Set of 15 bacterial species protects mice from Salmonella as effectively as natural gut microbiota – Doug Powell – Barfblog

Surprise: Probiotics Don’t Do Much At All For Our Gastrointestinal Health – Drew Smith – Forbes

#BacteriaArePlural: Ravenous Bacteria Eats Poop and Produces Power – Rhett Jones – Gizmodo

Gut bacteria study could lead to new Crohn’s treatments, researchers say – CBC News

Hospital Microbiology Testing Market Positive Long-Term Growth Outlook 2016 – 2024 – Digital Journal

Bik’s Non-Microbiology Picks

Researchers discover most winter boots are too slippery to walk safely on icy surfaces – EurekAlert

 

November 23, 2016

Posted on by

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

November 21, 2016

Posted on by

Why is the human vaginal microbiome unique, multiple sclerosis, fiber-deprived gut microbes eating mucus, vertical structure of the phyllospere, cave microbiome, resistome.

Pregnancy and early life

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study – Kaori Tachibana – Journal of Diabetes Investigation

Human vaginal microbiome

Lactobacilli Dominance and Vaginal pH: Why is the Human Vaginal Microbiome Unique? – Elizabeth A. Miller – Frontiers in Microbiology

Human gut microbiome

Prevalence of Small Intestinal Bacterial Overgrowth in Multiple Sclerosis: a Case-Control Study from China – Yongbo Zhang – Journal of Neuroimmunology

MyNewGut: Insulin resistance as key factor for linking modulation of gut microbiome to health claims and dietary recommendations to tackle obesity – Stoffer Loman -Trends in Food Science & Technology

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Review: Microbiome and nutrition in autism spectrum disorder: current knowledge and research needs – Kirsten Berding – Nutrition Reviews

Review: Th Role of Short-Chain Fatty Acids in Kidney Injury Induced by Gut-derived Inflammatory Response – Wei Huang – Metabolism

Review: Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition – Keerati Wanchai – The American Journal of the Medical Sciences

Animal and in vitro experiments

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility – Mahesh S. Desai – Cell
Editorial: Veggies and Intact Grains a Day Keep the Pathogens Away – Francesca S. Gazzaniga – Cell
Press: High-fiber diet keeps gut microbes from eating the colon’s lining, protects against infection, animal study shows – Science Daily

Coevolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection – Suzanne A. Ford – Molecular Ecology

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection – Yixin H. Ye – Journal of Invertebrate Pathology

Modulation of the cytokine profile in Caco-2 cells by faecal lactobacilli and bifidobacteria from individuals with distinct dietary habits – Diomira Luongo – Cytokine

An Alteration in the Cecal Microbiota Composition by Feeding of 1-Kestose Results in a Marked Increase in the Cecal Butyrate Content in Rats – Takumi Tochio – PLOS ONE

Animal microbiome

Proteome data on the microbial microbiome of grasshopper feces – Nico Jehmlich – Data in Brief

Plant, root, and soil microbiome

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing – Ayako Izuno – PLOS ONE

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities – Rafal Zgadzaj – PNAS

Press: Nitrogen-fixing symbiosis is crucial for legume plant microbiome assembly – EurekAlert

Influence of salt tolerant Trichoderma spp. on growth of maize (Zea mays) under different salinity conditions – Krishna Kumar – Journal of Basic Microbiology

Review: Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review – Abdelaal Shamseldin – Symbiosis

Review: Forest microbiome: diversity, complexity and dynamics – Petr Baldrian – FEMS Microbiology Reviews

Review: The cave microbiome as a source for drug discovery: reality or pipe dream? – Soumya Ghosh – Biochemical Pharmacology

Extremophile microbiome

Opinion: Colonization of Black Smokers by Hyperthermophilic Microorganisms – Reinhard Wirth – Trends in Microbiology

Food microbiology

Biofilms formed by microbiota recovered from fresh produce: Bacterial biodiversity, and inactivation by benzalkonium chloride and enterocin AS-48 – Mª José Grande Burgos – LWT – Food Science and Technology

Metabolomics

Comparative in silico analysis of butyrate production pathways in gut commensals and pathogens – Swadha Anand – Frontiers in Microbiology

Resistome

Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria – Sabrina Duranti – Applied and Environmental Microbiology

Review: Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
– José L. Martínez – Annals of the New York Academy of Sciences

Microbes in the news

I got my gut sequenced – and found out I need to go to the dentist – Liam Mannix – Sydney Morning Herald

Bighorn sheep transfer OK’d despite concerns about disease – Brett French – Missoulian
http://missoulian.com/news/state-and-regional/bighorn-sheep-transfer-ok-d-despite-

High-Fat Diets Alter Gut Microbiota, Leading to Increased Choroidal Neovascularization – Dava Stewart – HCP Live

Student scientists engineer bacteria to break down plastic, hope to help clean Baltimore harbor – Scott Dance – The Baltimore Sun

Soil bacteria helps protect rice plants from arsenic and fungus. ‘Cocktail’ of soil bacteria can protect rice plants from deadly forces – Science Daily
Bacteria Might Be Able To Help Rice Affected By Fungus – Rodney Rafols – iTechPost

November 19, 2016

Posted on by

Metformin and diabetes, lizards, Brazilian tree phyllosphere, Amazonian dark earth, air pollution in China, microbiomes of ice cream and cannabis.

General microbiome

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History – Andrew W. Brooks – PLOS Biology

Review: A place for host–microbe symbiosis in the comparative physiologist’s toolbox – Kevin D. Kohl – Journal of Experimental Biology

Human skin and wound microbiology

Review: Cooperative Evolutionary Strategy between the Bacteriome and Mycobiome – Mahmoud Ghannoum – mBio

Human gut microbiome

Metformin Is Associated With Higher Relative Abundance of Mucin-Degrading Akkermansia muciniphila and Several Short-Chain Fatty Acid–Producing Microbiota in the Gut – Jacobo de la Cuesta-Zuluaga – Diabetes Care

News: Metformin Alters Gut Microbiota Composition in Diabetes – Doctors Lounge

Review (Blastocystis) : Modulating the Gut Micro-Environment in the Treatment of Intestinal Parasites – Luis Vitetta – Journal of Clinical Medicine

Review: Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome – Pedro Morgado – F1000 Research

Microbes in blood, urine, and tissue

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis – Benjamin Lelouvier – Hepatology

Review: The Urinary Tract Microbiome in Health and Disease – Isabel M. Aragón – European Urology Focus

Animal experiments

A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats – Kelsey H. Collins – Scientific Reports

Animal microbiome

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions, and transmission – Kevin D. Kohl – Molecular Ecology

In liver, not in feces: Metagenomic Evaluation of Bacteria from Voles – Katja A. Koskela – Vector-Borne and Zoonotic Diseases

Plant, root, and soil microbiome

Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy – M.R. Lambais – Microbial Ecology

Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil – Leandro Nascimento Lemos – Genomics Data

Metal-resistant rhizobacteria isolates improve Mucuna deeringiana phytoextraction capacity in multi-metal contaminated soils from a gold mining area – Cácio Luiz Boechat – Environmental Science and Pollution Research

Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil
Adina Howe – PLOS ONE

The nutrient preference of plants influences their rhizosphere microbiome – Feng Cai – Applied Soil Ecology

Effect of microbial-based inoculants on nutrient concentrations and early root morphology of corn (Zea mays) – Pamela Calvo – Journal of Plant Nutrition and Soil Science

The impact of winter legume and cereal cover crops on rhizosphere microbial communities of subsequent vegetable crops for contrasting crop decline – L.M. Manici – Biological Control

Impacts of protected colonial birds on soil microbial communities: When protection leads to degradation – María T. Domínguez – Soil Biology and Biochemistry

Water and pollution microbiome

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera – Megan M. Morris – Frontiers in Microbiology

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater – Dongping Wang – Microbiology Open

Screening and In Situ Monitoring of Potential Petroleum Hydrocarbon Degraders in Contaminated Surface Water – Bulent Icgen – Clean Soil Air Water

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling – D.T. McCarthy – Water Research

Air microbiology

Airborne particulate matter pollution in urban China: A chemical mixture perspective from sources to impacts – Ling Jin – National Science Review

Review: Monitoring of the airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios – Andrés Núñez – International Microbiology

Review: Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments – Andrés Núñez – International Microbiology

Food and cannabis microbiology

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests – Kevin McKernan – F1000 Research

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak – Andrea Ottesen – BMC Microbiology

Bioinformatics

[PDF] A small-sample multivariate kernel machine test for microbiome association studies – Xiang Zhan – Fred Hutch Research

More microbiology

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems – Adrian G. Patterson – Molecular Cell

Bacteria communicate to ramp up collective immune response to viral threats – Science Daily

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space – Luis Zea – PLOS ONE

Alabama researcher helps solve mystery of runaway bacteria on spaceships – AL.com

Microbes in the news

Podcast: This Week in Microbiology: microbial DNA found on ATM machines in New York City, and how hydraulic fracturing, or fracking, alters microbial ecosystems deep in the Earth – TWIM

One swab from the surface of your smartphone can tell scientists all about your lifestyle
– Karen Turner – Washington Post

This bacteria is getting harder for kids to fight – Mashable

Armpit Bacteria Transplants Could Save Us From Our Stink – Kaleigh Rogers – Motherboard

Worrying traces of resistant bacteria in air – EurekAlert

 

Science, publishing, and career

An Open Letter from and to Female Scientists – Kelly Ramirez – Scientific American
500 Women Scientists: An open letter from women of science

Who Will Advise Trump on Science? – Ed Yong – The Atlantic

 

 

 

November 18, 2016

Posted on by

Pathogens in rheumatoid arthritis, Staph in hog workers, pathogens in bat guano, host colonization determinants, microbes on New York ATM keypads.

Human oral microbiome

Clinical effects of probiotics containing Bacillus species on gingivitis: a pilot randomized controlled trial – B. Alkaya – Journal of Periodontal Research

Human respiratory microbiome

Livestock-Associated, Antibiotic-Resistant Staphylococcus aureus Nasal Carriage and Recent Skin and Soft Tissue Infection among Industrial Hog Operation Workers – Maya Nadimpalli – PLOS ONE

Hog workers carrying livestock-related, drug-resistant bacteria may be developing skin infections – News Medical

Human gut microbiome

A method for automated pathogenic content estimation with application to rheumatoid arthritis – Xiaoyuan Zhou and Christine Nardini – BMC Systems Biology

Imbalance of bacteriome profiles within the Finnish Diabetes Prediction and Prevention study: Parallel use of 16S profiling and virome sequencing in stool samples from children with islet autoimmunity and matched controls – Ondrej Cinek – Pediatric Diabetes

Review: Diet, microorganisms and their metabolites, and colon cancer – Stephen J. D. O’Keefe – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota and functional diseases of the gastrointestinal tract – Nicola Imperatore – Minerva Gastroenterologica e Dietologlica

Animal experiments

Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16 – Joakim H. Bergström – PNAS

In bees: Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont – J. Elijah Powell – PNAS

A new pathway for the gut microbiota to modulate the brain: activation of pattern-recognition receptors by microbial products – P Zheng – Mol Psychiatry

The bacterial peptidoglycan-sensing molecule Pglyrp2 modulates brain development and behavior – T Arentsen – Mol Psychiatry

Animal microbiome

Bats: Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano – Sunil Banskar – Scientific Reports

Plant, root, and soil microbiome

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island – Jun Ling – PNAS

Built environment microbiome

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City – Holly M. Bik – mSphere

Food microbiome

Inferring the role of microorganisms in water kefir fermentations – Abigail Martínez-Torre – International Journal of Food Science & Technology

Microbes in the news

Australian Academy of Sciences announces 2017 honorific awardees, including infectious diseases professor Kathryn Elizabeth Holt

Common Skin Bacteria Could Save You From Other Skin Diseases – Monica U Santos – iTechPost
Skin bacterium releases enzyme that may protect against damage and disease – Catherine Paddock – Medical News Today

The Microbiome’s Role in Precision Medicine, with Jun Sun and Jack Gilbert – Kristen Thometz – WTTW

Microbes on the market

uBiome in the news: Startup will ‘DNA test’ your poop to analyze your gut health – Natural News

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – BusinessWire

November 12, 2016

Posted on by

Two papers on the detection of diseases by metabolomics of breaths or fecal gases, responses of soil bacteria to solar radiation and soil warming, genotyping of probiotics.

General microbiome

Special Issue on ‘Microbe–host interactions’ – Sven Hammerschmidt – FEBS Letters

Pregnancy and early life

Serum cathelicidin, nasopharyngeal microbiota, and disease severity among infants hospitalized with bronchiolitis – Kohei Hasegawa – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Feasibility of Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics: A Pilot Study – Xiaoling Zang – Journal of Proteome Research

Features of the bronchial bacterial microbiome associated with atopy, asthma and responsiveness to inhaled corticosteroid treatment – Juliana Durack – Journal of Allergy and Clinical Immunology

Human vaginal microbiome

“Murdochiella vaginalis” sp. nov., a new bacterial species cultivated from the vaginal flora of a woman with bacterial vaginosis – Khoudia Diop – Human Microbiome Journal

Human esophagus and stomach microbiome

Editorial: The microbiome as a potential biomarker for oesophageal adenocarcinoma – Julian A Abrams – The Lancet Gastroenterology & Hepatology

A non-endoscopic device to sample the oesophageal microbiota: a case-control study – Daffolyn R Fels Elliott – The Lancet Gastroenterology & Hepatology

Human gut microbiome

Irritable bowel syndrome and active inflammatory bowel disease diagnosed by faecal gas analysis – R. B. M. Aggio – Alimentary Pharmacology and Therapeutics

Review: Formation of propionate and butyrate by the human colonic microbiota – Petra Louis

Review: The Gut Microbiota : The Gateway to Improved Metabolism – Kristina B. Martinez – Gastroenterology Clinics of North America

Review: Regulation of the gut microbiome by inflammasomes – Grace Y. Chen – Free Radical Biology and Medicine

Review: The role of the microbiome in kidney stone formation – Mansi Mehta – International Journal of Surgery

Animal models

Giardia alters commensal microbial diversity throughout the murine gut – Nanelle R Barash – bioRxiv

Animal microbiome

Virus detection using metagenomic sequencing of swine nasal and rectal swabs – Ben M. Hause – J Swine Health Prod

Plant, root, and soil microbiome

Bacterial active community cycling in response to solar radiation and their influence on nutrient changes in a high altitude wetland – Veronica Molina – Frontiers in Microbiology

Land-use change under different climatic conditions: Consequences for organic matter and microbial communities in Siberian steppe soils – Norbert Bischoff – Agriculture, Ecosystems & Environment

Identifying the microbial taxa which consistently respond to soil warming across time and space – Angela M. Oliverio – Global Change Biology

The drivers underlying biogeographical patterns of bacterial communities in soils under sugarcane cultivation – Ademir Durrer – Applied Soil Ecology

Editorial: A small soil bacterium dominates – Ursula Hofer – Nature Reviews Microbiology

Editorial/Review: The Role of Microbial Communities in Tropical Ecosystems – Silvia Pajares – Frontiers in Microbiology

Water microbiome

Cyanobacteria in lakes on Yungui Plateau, China are assembled via niche processes driven by water physicochemical property, lake morphology and watershed land-use – Jingqiu Liao – Scientific Reports

Implications of Ecological Niche Differentiation in Marine Bacteria for Microbial Management in Aquaculture to Prevent Bacterial Disease – Tom Defoirdt – PLOS Pathogens

Bacterial composition, abundance and diversity in fish polyculture and mussel–fish integrated cultured ponds in China – Xiafei Zheng – Aquaculture Research

Food microbiome

Diversity study of microbial community in bacon using metagenomic analysis – Langbo Yi – Journal of Food Safety

Probiotics

Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases – Wesley Morovic – Frontiers in Microbiology

Review: Weight gain by gut microbiota manipulation in productive animals – Emmanouil Angelakis – Microbial Pathogenesis

Viruses and phages

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs – Yi Zheng – Virology

Metabolomics

Book Chapter: A Mathematical Perspective on Microbial Processes in Earth’s Biogeochemical Cycles – Christof Meile – Mathematical Paradigms of Climate Science
Bioinformatics and metagenomics

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome – José L. Martínez – Annals of the New York Academy of Sciences

More microbiology

The planktonic relationship between fluid-like electrodes and bacteria: wiring in motion
– Sara Tejedor Sanz – ChemSusChem

Experimental study and Random Forest prediction model of microbiome cell surface hydrophobicity – Yong Liu – Expert Systems with Applications

Microbes in the news

uBiome CEO Dr. Jessica Richman to Deliver Opening Keynote at American Medical Informatics Association Symposium – PR web

The impact of the rhizosphere microbiota on root system development and tolerance to environmental constraints in cereals – International Center for Biosaline Agriculture

Miami wants to introduce MORE mosquitoes to fight Zika: Officials considers bringing in bacteria-infected insects to stop spread of virus – Daily Mail

Bruker Moving Into PCR-Based Testing to Expand Clinical Microbiology, MALDI Biotyper Offerings – Genome Web