Category Archives: Human gut

December 15, 2016

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Preannouncement of the second SF Bay Area Microbiome Meetup in January, enteric dysfunction in Malawian children, gastric microbiota in twins, Antarctic fish, soil of a medieval foundry.

Events

Preannouncement: 2nd SF Bay Area Microbiome Meetup – January 31, 2017 – Illumina, San Francisco – SF Biome

3rd Translational Microbiome Conference – April 11-13, 2017, Boston

Human gut microbiome

Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children – M. Isabel Ordiz – Am J Trop Med Hyg

Characterization of Gastric Microbiota in Twins – Quanjiang Dong – Current Microbiology

Faecal Carriage of Gram-Negative Multidrug-Resistant Bacteria among Patients Hospitalized in Two Centres in Ulaanbaatar, Mongolia – Bayaraa Baljin – PLOS ONE

Lifestyle and geographic insights into the distinct gut microbiota in elderly women from two different geographic locations – Ji-Hee Shin – Journal of Physiological Anthropology

Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals – Marco Toscano – Digestive and Liver Disease

Review: The intestinal microbiota in allogeneic hematopoietic cell transplant and graft-versus-host disease – Anna Staffas – Blood

Review: A story of metformin-butyrate synergism to control various pathological conditions as a consequence of gut microbiome modification: Genesis of a wonder drug? –
Kunal Maniar – Pharmacological Research

Animal models

Selective photoantisepsis – David M. Harris – Lasers in Surgery and Medicine

Press: Laser Treatments Shown Effective in Killing Bacteria That Cause Dental Disease – Photonics

Induction of FXR signaling in germ-free mice colonized with a human microbiota – Annika Wahlström – Journal of Lipid Research

Modulation of urinary siderophores by the diet, gut microbiota and inflammation in mice –
Xia Xiao – Journal of Nutritional Biochemistry

Value added by Spirulina platensis in two different diets on growth performance, gut microbiota, and meat quality of Japanese quails – Mohamed S. Yusuf – Veterinary World

Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal – Sebastián Díaz – Parasites & Vectors

Dietary Keratan Sulfate from Shark Cartilage Modulates Gut Microbiota and Increases the Abundance of Lactobacillus spp. – Qingsen Shang – Marine Drugs

New insights into the role of the porcine intestinal yeast, Kazachstania slooffiae, in intestinal environment of weaned piglets – Vladimir Urubschurov – FEMS Microbiology Ecology

Animal microbiome

The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis – Wei Song – BioMed Research International

Plant, root, and soil microbiome

It is elemental: Soil nutrient stoichiometry drives bacterial diversity – Manuel Delgado-Baquerizo – Environmental Microbiology

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression – Jie Hu – mBio

Composition of endophytic fungal community associated with leaves of maize cultivated in south Brazilian field – Vivian J. Szilagyi-Zecchin – Acta Microbiologica et Immunologica Hungarica

Vegetation type and layer depth influence nitrite-dependent methane-oxidizing bacteria in constructed wetland – Mengxi Yang – Archives of Micobiology

Water and extremophile microbiome

Nitrate addition has minimal short-term impacts on Greenland ice sheet supraglacial prokaryotes – Karen A. Cameron – Environmental Microbiology Reports

Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis – Anwesha Ghosh – Genomics Data

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics – Luciana Principal Antunes – Scientific Reports

Pollution microbiology

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA – Feng Shen – Scientific Reports

Paleomicrobiology to investigate copper resistance in bacteria: Isolation and description of Cupriavidus necator B9 in the soil of a medieval foundry – David C. Gillan – Environmental Microbiology

More microbiology

Stochastic Model for Direction Changes of Swimming Bacteria – Guido Fier – bioRxiv

Microbes in the news

Pitt study links cystic fibrosis lung inflammation to opportunistic bacteria – Lydia Nuzum – BizJournals

December 14, 2016

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Gaia and her microbiome, a walk in the park, ancient teeth, fillies, bats, ticks, frogs, moss, and high-altitude potatoes.

General microbiome

Gaia and Her Microbiome – John F. Stolz – FEMS Microbiology Ecology

Human oral microbiome

Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth – Nicolás Rascovan – NPJ Biofilms and Microbiome

Influences of pH and iron on the salivary microbiome in individuals with and without caries – Jianye Zhou – Applied and Environmental Microbiology

Human gut microbiome

Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus – Xiaokai Wang – Antonie van Leeuwenhoek

Animal experiments

Intense Exercise and Aerobic Conditioning Associated with Chromium or L-Carnitine Supplementation Modified the Fecal Microbiota of Fillies – Maria Luiza Mendes de Almeida – PLOS ONE

 

Animal microbiome

Mosquitoes: Diversity of Cultivable Midgut Microbiota at Different Stages of the Asian Tiger Mosquito, Aedes albopictus from Tezpur, India – Kamlesh K. Yadav – PLOS ONE

Bats: Microbiome of the sexual scent organ of Leptonycteris yerbabuenae – Osiris Gaona – PeerJ

Ticks: Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California – Nikos Gurfield – PeerJ

Frogs: Environmental fluctuations and host skin bacteria shift survival advantage between frogs and their fungal pathogen – Ana V Longo – ISME Journal

Plant, root, and soil microbiology

Discovery of polyesterases from moss-associated microorganisms – Christina Andrea Müller – Applied and Environmental Microbiology

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil – Honggui Wang – Soil Biology and Biochemistry

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development – Stefan Pfeiffer – FEMS Microbiology Ecology

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures – Senta Heiss-Blanquet – PLOS ONE

Effects of root exudates of woody species on the soil antierodibility in the rhizosphere in a karst region, China – Zhen hong Wang – PeerJ Preprint

Water and extremophile microbiome

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf – Jean-David Grattepanche – PLOS ONE

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China – Yongjuan Chen – Applied Microbiology and Biotechnology

Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes – Alejandro Arce-Rodríguez – Extremophiles

Quantification of basal ice microbial cell delivery to the glacier margin – Mario Toubes-Rodrigo – Biogeosciences Discuss

Microbial Diversity of Source and Point-of-Use Water in Rural Haiti – A Pyrosequencing-Based Metagenomic Survey – Nabanita Mukherjee – PLOS ONE

Virus-host infection dynamics of marine single-celled eukaryotes resolved from metatranscriptomics – bioRxiv

Pollution

The Biologists’ Forum: Environmental microbial community analysis methods as applied to bioremediation – Hadassa Shira Guttman – BIOS

Food microbiology

Determination of Fungal Community Diversity in Fresh and Traditional Chinese Fermented Pepper by Pyrosequencing – Lingyan Zhao – FEMS Microbiology Letters

Metagenomics

Using Bacterial Genomes and Essential Genes for the Development of New Antibiotics – Francisco R. Fields – Biochemical Pharmacology

Antibiotic discovery is a walk in the park – Louis-Félix Nothias – PNAS

Metabolomics

Book: Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology – Editors: David J. Beale, Konstantinos A. Kouremenos, Enzo A. Palombo – Springer

Microbes in the news

Scientists trap bacteria with optical tractor beam.”The principle underlying this laser beam is similar to the concept to be found in the television series ‘Star Trek,'” said researcher Thomas Huser –  Brooks Hays – UPI

Researchers find bacterial protein that boosts insulin-producing cells in zebrafish – Science Daily

A $5 fix for a nasty parasite: Attachment of Cryptosporidium parvum oocysts to environmental biofilms – EurekAlert

Increasing Product Recalls and Growing Consumer Concerns are Driving the Global Industrial Microbiology Market – Medgadget

 

 

December 13, 2016

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Top 25 Microbiology Blog and Website List for Microbiologists – What a great list! But I’m a bit sad that I did not make it. But, lots of other great blogs luckily are listed here. Meantime, I will just carry the “I did not make it” badge.

Jobs

Lecturer in Oral Microbiology – University of Bristol

Human gut microbiome

Gut microbiome in children with enthesitis-related arthritis in a developing country and the effect of probiotic administration – A. Aggarwal – Clinical & Experimental Immunology

Review: Role of the Microbiota in Colorectal Cancer: Updates on Microbial Associations and Therapeutic Implications – Olivia I. Coleman – BioResearch

Paper Hopes To Link Diet, Gut Microbiome And Colorectal Cancer – Science2.0

Animal microbiome

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community  – Nir Friedman – Environmental Microbiology

Potential role of ectoparasites (Zeuxapta seriolae and Caligus lalandei) in the transmission of pathogenic bacteria in yellowtail kingfish Seriola lalandi, inferred from cultivable microbiota and molecular analyses – F A Sepúlveda – Journal of Fish Diseases

Microbe in the news

“Eight minutes of struggling arthropods set to Beethoven’s Moonlight Sonata” – Bacteria Help Pitcher Plants Trap Prey –  Elizabeth Preston – Discover Magazine

Orange ‘ooze’ in Beaver Brook a harmless bacteria, city officials say – Xander Landen – Sentinel Source

Why are we so passionate about the smiling poop emoji? – Samantha Selinger-Morris – ABC

Researcher rethinks lactic acid bacteria – Stevie Kenyon – Daily Cardinal

Video: The Microbiome and Outcomes After Allogeneic Transplant – Robert Jenq – Cancer Network

Digging Deep for New Bacteria – Scientists find a whole ecosystem in fracking water – Eric Betz – Discover

Your head or your gut? – Justin D. Glenn – Labnews

Make-up of equine gut bacteria altered by exercise, study shows – Horse Talk

Bacteria Beef Up New Tree of Life. The new tree of life includes previously unknown species throughout the bacterial branches – Jonathon Keats – Discover

Researchers’ findings offer clue on how to block biofilm shields of bacterial infections – Science Daily

Microbes on the market

 

Biofilm tech wins CTAQ award – Food Quality News

C3J Therapeutics Unveils Development of Two New Product Formulations of Lead Candidate C16G2 for Prevention of Dental Caries – Nasdaq

The Detox Me Action Kit by Silent Spring Institute – IndieGoGo

DNA Biohackers Are Giving The FDA A Headache With Glow-In-The-Dark Booze. A biohacker thought he could sell something cool without consequences. The FDA thought otherwise. – Stephanie M. Lee – Buzzfeed

Product News: Rainin Pos-D™ Pipettes Allow Environmental Microbiology Researchers to Investigate Biodegradation of Oil  – Select Science

December 12, 2016

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Review on human milk microbiome, oral microbiome changes in seasonal athletes, gut microbiome and bipolar disorder.

Jobs

Assistant Professor In Quantitative Ecology or Evolution of Microbes – UCLA – MicroBEnet

Pregnancy and early life

Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy – Ekaterina Avershina – Journal of Allergy and Clinical Immunology

* Review: Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk – Michelle K McGuire – Current Opinion in Biotechnology

Human respiratory microbiome

Review: Viral–bacterial co-infections in the respiratory tract – Lauren O Bakaletz – Current Opinion in Microbiology

Human oral microbiome

* I was wondering if testing same group of athletes participating in 2 different sports could not be confounded with seasonal effects of maybe different study loads during the different year. But no access to the paper, so can not see details. Elevated salivary IgA, decreased anxiety, and an altered oral microbiota are associated with active participation on an undergraduate athletic team – Ashley L. Lamb – Physiology & Behavior

Human gut microbiome

* The gut microbiome composition associates with bipolar disorder and illness severity – Simon J. Evans – Journal of Psychiatric Research

Letter of the Editor: A Microbiome Assessment of Medical Marijuana – George Thompson III – Clinical Microbiology and Infection

Review: Archaea: essential inhabitants of the human digestive microbiota – Vanessa Demonfort Nkamga – Human Microbiome Journal

Animal experiments

Application of a dynamic gastrointestinal in vitro model combined with a rat model to predict the digestive fate of barley dietary fibre and evaluate potential impact on hindgut fermentation – Cristina Teixeira – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

Characterization and identification of microbial communities in bovine necrotic vulvovaginitis – N.Y. Shpigel – The Veterinary Journal

Crab: Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus – Ting-Lan Zeng – Chinese Journal of Analytical Chemistry

Plant, root, and soil microbiome

Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata – Suvendu Das – Journal of Hazardous Materials

Food microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Bioinformatics and metagenomics

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics – Karel Sedlar – Computational and Structural Biotechnology Journal

Microbes in the news

Predatory bacteria used to release bioplastics – Tim Sandle – Digital Journal

The Secret Soviet Virus That Helps Kill Bacteria. Antibiotic resistance is threatening to render antibiotics useless, but scientists may have found their answer in bacteria-eating viruses. – Trace Dominguez – Seeker

Bacteria found in close to two-thirds of NZ supermarket chicken – TV New Zealand

Science, publishing, and career

This would not be my headline choice: Trump says ‘nobody really knows’ if climate change is real – Juliet Eilperin – Washington Post

December 10, 2016

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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

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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 8, 2016

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Bacteria in upper GI tract, visceral pain, stromatolites, polluted urban soils.

Pregnancy and early life

Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants – S. S. Al-Shehri – Scientific Reports

Cesarean birth is not associated with early childhood body mass index – L. G. Smithers – Pediatric Obesity

Human skin microbiome

Culture-Based Screening of Aerobic Microbiome in Diabetic Foot Subjects and Developing Non-healing Ulcers – Saba Noor – Frontiers in Microbiology

Human gut microbiome

* The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection – Christian Schulz – Gut

Elderly patients have an altered gut-brain axis regardless of the presence of cirrhosis – Jasmohan S. Bajaj – Scientific Reports

Review: HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation – Gootenberg, David B – Current Opinion in Infectious Diseases

Review: A Perspective on Brain-Gut Communication: The American Gastroenterology Association and American Psychosomatic Society Joint Symposium on Brain-gut Interactions and the Intestinal Microenvironment – Aroniadis, Olga C. – Psychosomatic Medicine

Review: Mechanisms of Cross-talk between the Diet, the Intestinal Microbiome, and the Undernourished Host – Helene Velly – Gut Microbes

* Review: The Gut Microbiota as a Key Regulator of Visceral Pain – O’ Mahony, Siobhain M – Pain

Crystal ball : Microbiomes, metabolic errors and detection of performance enhancing drug abuse – Environmental Microbiology Reports

Animal and in vitro models

Masked trichothecene and zearalenone mycotoxins withstand digestion and absorption in the upper GI tract but are efficiently hydrolyzed by human gut microbiota in vitro – Silvia W. Gratz – Molecular Nutrition & Food Research

Light/Dark Shifting Promotes Alcohol-Induced Colon Carcinogenesis: Possible Role of Intestinal Inflammatory Milieu and Microbiota – Faraz Bishehsari – International Journal of Molecular Sciences

Colonic luminal microbiota and bacterial metabolite composition in pregnant Huanjiang mini-pigs: effects of food composition at different times of pregnancy – Xiang-feng Kong – Scientific Reports

Animal microbiome

Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria – Olga L. Mayorga – Frontiers in Microbiology

Plant, root, and soil microbiome

Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function – Tanya E. Cheeke – New Phytologist

Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas – Garima Dubey – 3 Biotech

Clay-to-Carbon Ratio Controls the Effect of Herbicide Application on Soil Bacterial Richness and Diversity in a Loamy Field – H. M. L. I. Herath – Water, Air, & Soil Pollution

* Microorganisms isolated from polluted urban soils highly effectives in degrading recalcitrant pesticides – Liliana Rocío Botero-Botero

Review: The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective – Panagiotis Gkorezis – Frontiers in Microbiology

Review: Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems – Thomas Bell – Proceedings of the Royal Society B

Water and extremophile microbiome

* Participation of algal–bacterial community in the formation of modern stromatolites in Cock Soda Lake, Altai Region – O. S. Samylina – Paleontological Journal

Microbial mediated arsenic biotransformation in wetlands – Si-Yu Zhang – Frontiers of Environmental Science & Engineering

More microbiology

Antibiotic resistance in the wild: an eco-evolutionary perspective – Teppo Hiltunen – Philosophical Transactions of the Royal Society B

Microbes in the news

New polymer £5 notes are three times cleaner and hold less bacteria, scientists have found
Less bacteria sticks to the new polymer notes as it is revealed the old paper notes were among the dirtiest in Europe – Jennifer Hale – The Sun

The Coolest Thing Bio350 Micronauts Learned in Fall 2016 – Mark O. Martin – Microbes Rule Blogspot

Glow-in-the-dark bugs bring art to life: Dr Siouxsie Wiles has teamed up with artists and schoolchildren for this weekend’s SciGlow exhibition at Auckland’s Silo Park – Jamie Morton – NZ Herald

Nearly 2 Million Pounds Of Chicken Recalled For Possible Bacteria – CBS

Magnetic purification of blood ‘pulls out’ the bacteria – Nanowerk

Microbes on the market

uBiome Announces SmartBiomeTM, a Novel Comprehensive Metagenomic Deep Sequencing Research Platform – PR Web

Synlogic CEO downplays ‘yuck factor’ of the microbiome – Big News Network

AGA and The Dannon Company Recognize Microbiome Leader Dr. Gary Wu – BusinessWire

Gut feelings: How the microbiome may affect mental illness and interact with treatment – MedicalXpress

December 7, 2016

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Microbiota of migratory birds, blue fungus living in snow, migrating from SSU rRNAs to metagenomics.

Jobs

Awesome job at awesome institute: Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Human gut microbiome

Special issue of Trends in Food Science & Technology; several papers have appeared here before but worth checking out: Unravelling the role of the gut microbiome in energy balance and brain development and function: the European project MyNewGut

Review: Homeostasis of the Gut Barrier and Potential Biomarkers – Jerry M Wells – American Journal of Physiology, Gastrointestinal and Liver Physiology

Review: Challenges in simulating the human gut for understanding the role of the microbiota in obesity – M. Aguirre – Beneficial Microbes

Animal models

Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys – Xuan He – mSystems

Review: Dissecting the interplay between intestinal microbiota and host immunity in health and disease: Lessons learned from germfree and gnotobiotic animal models – Ulrike Fiebiger – European Journal of Microbiology and Immunology

Animal microbiome

* Changes in gut microbiota of migratory passerines during stopover after crossing an ecological barrier – William B. Lewis – The Auk

Plant, root, and soil microbiome

* Microbial Community Structure and Function of Soil following Ecosystem Conversion from Native Forests to Teak Plantation Forests – Vidya De Gannes – Frontiers in Microbiology

Drought tolerance of bioenergy grass Saccharum spontaneum L. enhanced by arbuscular mycorrhizae – P.P. Mirshad – Rhizosphere

Perspective: Microbiome selection could spur next-generation plant breeding strategies – Murali Gopal – Frontiers in Microbiology

Water and extremophile microbiome

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean – Rene M. Boiteau – PNAS

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments, Lake Baikal – S. M. Chernitsyna – Microbiology

Dampened copepod-mediated trophic cascades in a microzooplankton-dominated microbial food web: A mesocosm study – Bernadette Pree – Limnology and Oceanography

* Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica – Graciéle C. A. de Menezes – Extremophiles

Temporal variability of bacterial communities in cryoconite on an Alpine glacier – Andrea Franzetti – Environmental Microbiology Reports

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP) – Michael Morando – Frontiers in Microbiology

Pollution microbiology

Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit – V. V. Kadnikov – Microbiology

Metagenomics and bioinformatics (viruses too)

MEGARes: an antimicrobial resistance database for high throughput sequencing – Steven M. Lakin – Nucleic Acids Research

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center – Alice R. Wattam – Nucleic Acids Research

Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences – Nathan A. Ahlgren – Nucleic Acids Research

*  Crystal Ball: Migrating SSU rRNA gene surveys to the metagenomics era – Josh D. Neufeld – Environmental Microbiology Reports

Techniques

DNA extraction from benthic Cyanobacteria: comparative assessment and optimization – V. Gaget – Journal of Applied Microbiology

Microbial ecology

Microbial Community Coalescence for Microbiome Engineering – Matthias C. Rillig – Frontiers in Microbiology

More microbiology

How to Define Pathogenicity, Health, and Disease? – Mauno Vihinen – Human Mutation-Variation, Informatics, and Disease

Crystal Ball: Accessories make the microbe – Lisa Y. Stein – Environmental Microbiology Reports

Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data – Shiori Sagawa – bioRxiv

Microbes in the news

With my former Stanford co-worker Fiona Strouts: New farmers’ market baker knows art, science of bread-making. Stanford fellow brings baking know-how to Portola Valley farmers’ market – Dave Boyce – Mountain View Voice

New Mechanism to Control Human Viral Infections Discovered – Sean Nealon – University of California Riverside

Uterine microbiota play a key role in implantation and pregnancy success in in vitro fertilization – EurekAlert (see digest October 12)

Understanding microbiome impact on pig health – National Hog Farmer

Syphilis is coming back – Juha Wahlstedt – Clinical Laboratory Blogspot

December 5, 2016

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Contraceptives and the vaginal microbiome, Ralstonia and CF outcome, Alzheimer’s, helminths in cats, the Mississippi River.

General microbiome and ecology

Review: Disentangling Interactions in the Microbiome: A Network Perspective – Mehdi Layeghifard – Trends in Microbiology

Book Chapter: Chapter 4 – The Human Microbiome – Jacquelyn S. Meisel – Genomic and Precision Medicine (Third Edition): Foundations, Translation, and Implementation – Chp

Pregnancy and early life

Maternal health and the placental microbiome – Elise Pelzer – Placenta

Human vaginal microbiome

* Effects of Combined Oral Contraceptives, Depot Medroxyprogesterone Acetate, and the Levonorgestrel-releasing Intrauterine System on the Vaginal Microbiome – J. Paul Brooks – Contraception

Review: Lactobacillus iners: Friend or Foe? – Mariya I. Petrova – Trends in Microbiology

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

* Ralstonia mannitolilytica in cystic fibrosis: A new predictor of worse outcomes – I. Coman – Respiratory Medicine Case Reports

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing – Claire L. McMurray – Microbiome

Human oral microbiome (also: gut / viruses)

Transmission of viruses via our microbiomes – Melissa Ly – Microbiome

Review: Endodontic Microbiology and Pathobiology : Current State of Knowledge – Ashraf F. Fouad – Dental Clinics of North America

Human gut microbiome

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies – Euan Watt – Microbiome

Review: Crohn’s disease – Joana Torres – The Lancet

Review: The Microbiome in Neurogastroenterology – Geoffrey A. Preidis – Pediatric Neurogastroenterology

Review: The endocrine vitamin D system in the gut – Antonio Barbáchano – Molecular and Cellular Endocrinology

Microbes at nearly sterile sites

* Gram-negative bacterial molecules associate with Alzheimer disease pathology – Xinhua Zhan – Neurology

Press: Gram-negative bacteria may influence Alzheimer’s disease pathology – ScienceDaily

Animal and in vitro models

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota – A. Sloan Devlin – Cell Host & Microbe

Animal microbiome

* Helminth infections and gut microbiota – a feline perspective – Ana M. Duarte – Parasites & Vectors

Review: Defining the Core Microbiome in Corals’ Microbial Soup – Alejandra Hernandez-Agreda – Trends in Microbiology

Plant, root, and soil microbiome

Bacterial consortia inoculation mitigates the water shortage and salt stress in an avocado (Persea americana Mill.) nursery – Patricio J. Barra – Applied Soil Ecology

Heavy Metal Pollution Structures Soil Bacterial Community Dynamics in SW Spain Polluted Salt Marshes – Jennifer Mesa – Water, Air, & Soil Pollution

The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding – Eveline Adam – Plant and Soil

Tolerance of the forest soil microbiome to increasing mercury concentrations – Aline Frossard – Soil Biology and Biochemistry

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

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought – A. Mark Ibekwe – Science of the Total Environment

Cross-compatibility evaluation of plant growth promoting rhizobacteria of coconut and cocoa on yield and rhizosphere properties of vegetable crops – T.H Khadeejath Rajeela – Biocatalysis and Agricultural Biotechnology

Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under differing conditions – N.G. Inostroza – Letters in Applied Microbiology

Differences among Soil-Inhabiting Microbial Communities in Poa annua Turf throughout the Growing Season – Lisa A. Beirn – Corp Science

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake – Pu Shen – PLOS ONE

Water and extremophile microbiome

* Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect – Michael W Henson – bioRxiv

Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River – L. Vezzulli – Microbial Ecology

Identity, ecology and ecophysiology of planktic green algae dominating in ice‑covered lakes on James Ross Island (northeastern Antarctic Peninsula) – Linda Nedbalová

Built environment microbiome

Analysis of dark crusts on the church of Nossa Senhora do Carmo in Rio de Janeiro, Brazil, using chemical, microscope and metabarcoding microbial identification techniques – Christine Gaylarde – International Biodeterioration & Biodegradation

Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance – Elodie Aubertheau – Science of the Total Environment

More microbiology

Human to human transmission of arthropod-borne pathogens – Byron E Martina – Current Opinion in Virology

Techniques

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

Microbes in the news

uBiome Awards Microbiome Impact Grant to Explore Effects of Heavy Drinking and Smoking on Oral Microbiome – PR Web

Missing Link in Malaria Evolution Discovered in Historical Specimens – Ben Andrew Henry – The Scientist

Book review: The Human Microbiome Handbook, Jason Tetro, Emma Allen-Vercoe (Eds.). DEStech Publications (March 2016)– Laura M. Cox – Anaerobe

Our ideas about bacteria evolution are wrong – scientists make new discovery – Sandra Hajda – Inquisitr

Bacteria Hysteria

Soap company uses bacteria-coated billboards to prove how dirty your stuff is – Mashable

December 3, 2016, part 2

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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