Author Archives: eliesbik

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

December 3, 2016

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Metagenomic tracking of stool transplant success, circadian oscillations in host transcription, microbial fermentation and chocolate flavors, and a future vision of medicine and microbiome analysis.

Human skin microbiome

16S based microbiome analysis from healthy subjects’ skin swabs stored for different storage periods reveal phylum to genus level changes – Ingeborg Klymiuk – Frontiers in Microbiology

Human gut microbiome

* High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes – Sonny TM Lee- bioRxiv

Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis – Raul Y. Tito – Arthritis & Rheumatology

Animal models

* Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations – Christoph A. Thaiss – Cell

Circadian rhythms and the microbiome: Disrupting daily routine of gut microbes can be bad news for whole body – Richard G. “Bugs” Stevens – The Conversation

Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes – Nicholas P. Semenkovich – PNAS

Luminal contents from the gut of colicky infants induce visceral hypersensitivity in mice – H. Eutamène – Neurogastroenterology & Motility

Supplementation of oligofructose, but not sucralose, decreases high-fat diet induced body weight gain in mice independent of gustducin-mediated gut hormone release – Sandra Steensels – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Soil microbial communities influence seedling growth of a rare conifer independent of plant–soil feedback – Jessica L. Rigg – Ecology

Reduced snow cover alters root-microbe interactions and decreases nitrification rates in a northern hardwood forest – Patrick O. Sorensen – Ecology

Water microbiome

Grazers structure the bacterial and algal diversity of aquatic metacommunities – Julia Birtel – Ecology

Food microbiology

* Influence of Cocoa Hybrids on Volatile Compounds of Fermented Beans, Microbial Diversity during Fermentation and Sensory Characteristics and Acceptance of Chocolates – Igor Magalhães da Veiga Moreira – Journal of Food Quality

Evaluation of Bacterial Contamination Sources in Meat Production Line – Farzaneh Bakhtiary- Journal of Food Quality

Pre- and probiotics

* A future vision of medicine: Crystal Ball: A routine check-up at the digital medical centre – Kenneth N. Timmis – Microbial Biotechnology

Microbes in the news

Martha Carlin: A Visionary Citizen Scientist Changing Microbiome and Medical Research – Anne Estes – Mostly Microbes

7 ways The BioCollective Will Accelerate Microbiome Research and Change Medicine – Anne Estes – Mostly Microbes

Young Innovators: Bacteria may hold secret to oilsands remediation – Federica Giannelli – The Star Phoenix

This week in microbiology: TWiM 140: Small town, big science – MicrobeTV
Finding Mars on Earth: Chilean Hot Springs Provide New Clues to a Martian Mystery – Jeffrey Marlow – Discover Magazine

Parkinson’s linked to gut bacteria – Robert Ferris – CNBC

The Army’s looking into putting bacteria into its electronics. Army Research Lab scientists are collaborating with biologists – Ars Technica

Bad Body Odor? Try Putting More Bacteria Under Your Pits – Kyle Frischkorn – GQ

Researchers discover way to make surfaces less vulnerable to disease-causing bacteria – Phys.org

Calculating for the Future: Can Breweries Provide More STEM Jobs for Women? – Bryan Roth – Beer Advocate

December 2, 2016

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Role of microbiome in an animal model of Parkinson’s disease, benchmarking reveals false discoveries in microbiome studies, the microbes of Patagonia, and the new uBiome blog.

The  uBiome blog

* Handshakes: Sharing the Love, Sharing the Microbes – Julie Taylor – uBiome

Jobs

Assistant Professor in Microbial Systems Biology at U. Tennessee, Knoxville – MicroBE.net

Human vaginal microbiome

Informativeness of NGS Analysis for Vaginal Fluid Identification – Saverio Giampaoli – Journal of Forensic Sciences

Animal models

* Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease – Timothy R. Sampson – Cell

News: Axial Biotherapeutics Announces the Groundbreaking Discovery of a Biological Link Between the Gut Microbiome and Parkinson’s Disease Published in Cell – Businesswire
Gut check: Newest microbiome startup concentrates on autism, Parkinson’s disease – John Carroll – Endpoints News

Multiple paternity in a wild population of Armadillidium vulgare: influence of infection with Wolbachia? – V. Valette – Journal of Evolutionary Biology

Plant, root, and soil microbiome

Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential – Jennifer M. DeBruyn – GCB Bioenergy

Vertical zonation of soil fungal community structure in a Korean pine forest on Changbai Mountain, China – World Journal of Microbiology and Biotechnology

* Book: Biology and Biotechnology of Patagonian Microorganisms – Editors: Nelda Lila Olivera, Diego Libkind, Edgardo Donati – Springer

Bioinformatics

* Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies – Jonathan Thorsen – Microbiome

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography – Silvia Argimón – Microbial Genomics

More microbiology

Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases – Ryutaro Furukawa – Journal of Molecular Evolution

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite – Tatiana Yurchenko – Open Biology

High levels of antibiotic tolerance and persistence are induced by the commercial anti-microbial triclosan – Corey S Westfall – bioRxiv

Microbes in the news

A citizen science project studying the microorganisms fauna found at the tip of our tongue – Euroscientist

Knowledge of skin microbiome provides insights into dermatological conditions – Skin microbes perform harmful and beneficial functions – Louise Gagnon – Dermatology Times

Digital Microbes Could Give More Insight into Gut Health – Nutrition Horizon

Healthy Gut, Healthy Brain? Microbes and Brain Health Under the Microscope During Mind, Mood & Microbes Conference – PR Newswire

Doctors warn about lung illness attributed to bacteria in showers and hot baths – Catherine Bosley – Cleveland19

Microbes on the market

Microbiome CNS upstart launches with $19.15M Series A – Ben Adams – Fierce Biotech

Boston startup hopes to use bacteria to treat autism – Robert Weisman

December 1, 2016

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Bacteria associated with high BM frequency in Japanese, red wine intake, drought stress in hardwood trees, and a book on Archaea.

Human oral microbiome

Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children – Shan Jiang – Int J Mol Sci

Infections of sterile sites

Clinical metagenomics of bone and joint infections: a proof of concept study – Etienne Ruppe – bioRxiv

Human gut microbiome

* Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type – Kaihei Ok – BMC Microbiology

* Phylogenetic profile of gut microbiota in healthy adults after moderate intake of red wine – Elvira Barroso – Molecular Nutrition & Food Research

Intestinal dysbiosis is common in systemic sclerosis and associated with gastrointestinal and extraintestinal features of disease – Kristofer Andréasson – Arthritis Research & Therapy

Dysbiosis of fecal microbiota and high frequency of Citrobacter, Klebsiella spp., and Actinomycetes in patients with irritable bowel syndrome and gastroenteritis – Leila Ganji – Gastroenterology and Hepatology: From Bed to Bench

Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance – Heinsen F.-A. – Obesity Facts

Comparative Fingerprinting of the Human Microbiota in Diabetes and Cardiovascular Disease – Vamanu Emanuel – Journal of Medicinal Food

Review: Clinical implications of the microbiome in urinary tract diseases – Andreas Hiergeist – Current Opinion in Urology
Review and video: How does the microbiome affect liver disease? – Herbert Tilg – Clinical Liver Disease

Animal models

Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota – Jinmei Ding – Genetics Selection Evolution

Plant, root, and soil microbiome

* Soil microbial communities buffer physiological responses to drought stress in three hardwood species – Steven A. Kannenberg – Oecologia

Review: Prospects for biological soil-borne disease control: application of indigenous versus synthetic microbiomes – Mark Mazzola – Phytopathology

Biofilms

Eradication of Pseudomonas aeruginosa biofilms and persister cells using an electrochemical scaffold and enhanced antibiotic susceptibility – Sujala T Sultana – NPJ Biofilms and Microbiomes

Researchers develop novel wound-healing technology – Phys.org

Microbes in the news

Mulch your soil—inside and out – David R. Montgomery and Anne Biklé

If You Want To Improve Gut Health, New Research Says Taking A Probiotic Isn’t Enough – Gretchen Lidicker – MindBodyGreen

A race to turn trillions of our own bacteria into medical breakthroughs – CNBC

Scientists create comprehensive computational metabolic models for different gut microbes – News Medical

* Book: Archaea 83 Success Secrets – 83 Most Asked Questions On Archaea – What You Need To Know – Adam Mcdowell – Kobo

November 30, 2016

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Microbiota-mitochondria crosstalk in Crohn’s Disease, is there a brain microbiome, Akkermansia proteins, Koala retroviruses, New York City park soil microbiomes, gift-giving insects, mud volcanos, 2.5 billion-year-old microbial fossils.

Events

The Gut Institute Microbiome Event in Berkeley, 10/11 December– Gut Institute

General microbiome

Microbial Ecology: Where are we now? – Lisa A. Boughner – Journal of Postdoctoral Research

Human respiratory microbiome

Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients – Ashley D. Smith – PLOS ONE

Human skin microbiome

Towards a bacterial treatment for armpit malodour – Chris Callewaert – Experimental Dermatology

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

Human microbes in (nearly) sterile sites

* Lots of extraction controls in this study, but they were not sequenced, and hard to accept there are thriving bacterial communities in our brain: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis – W. G. Branton – Scientific Reports

Human gut microbiome

* Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Nature Communications

Changes in Intestinal Microbiota Following Combination Therapy with Fecal Microbial Transplantation and Antibiotics for Ulcerative Colitis – Dai Ishikawa – Inflammatory Bowel Diseases

Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism – Federica Gevi – Molecular Autism

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

Animal and in vitro models

* A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice – Hubert Plovier – Nature Medicine

Stable Host Gene Expression in the Gut of Adult Drosophila melanogaster with Different Bacterial Mono-Associations – Carolyn Elya – PLOS ONE

Checks and balances – microbiota shifts in immunosuppressed mice – W. Florian Fricke – Transplantation

Dual-specificity phosphatase 6 deficiency regulates gut microbiome and transcriptome response against diet-induced obesity in mice – Jhen-Wei Ruan – Nature Microbiology

Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota – Yuanyuan Lu – Scientific Reports

Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice – Tadasu Iizumi – Gut Pathogens

Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice – Gladys Ferrere – Journal of Hematology

Impact of red meat consumption on the metabolome of rats – Louise M. A. Jakobsen – Molecular Nutrition & Food Research

11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to western diet – Jethro S Johnson – Journal of Endocrinology

Microbiota induces expression of tumor necrosis factor in postnatal mouse skin – D. V. Yuzhakova – Biochemistry (Moscow)

Animal microbiome

* Phylogenetic diversity of Koala Retrovirus within a Wild Koala Population – K.J. Chappell – Journal of Virology

* Partitioning the effects of mating and nuptial feeding on the microbiome in gift-giving insects – Chad C. Smith – Environmental Microbiology Reports

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

Plant, root, and soil microbiome

* Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity – Zachary Charlop-Powers – PNAS

News: Metagenomics Hints at Natural Product Potential of Microbes in New York City Parks – Genome Web
Study: New York City Dirt Rich in Bacteria Related to Medical Treatments – Robert Lee Hotz

* Sulfur-oxidizing bacteria prior to the Great Oxidation Event from the 2.52 Ga Gamohaan Formation of South Africa -Andrew D. Czaja – Geology

Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls – Cynthia M. Kallenbach – Nature Communications

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium – Alexander B. Chase – Frontiers in Microbiology

Molecular phylogeny, diversity, community structure, and plant growth promoting properties of fungal endophytes associated with the corms of saffron plant: An insight into the microbiome of Crocus sativus Linn. – Zahoor Ahmed Wani – Fungal Biology

Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load – Marie L. Davey – Molecular Ecology

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field – Yuan Liu – Frontiers in Microbiology

Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing – Lidita Khandeparker – Ecological Indicators

Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management – Carla Marisa Reis Varanda – Fungal Biology

Shifting patterns of microbial N-metabolism across seasons in upland Alaskan tundra soils – Shawna McMahon – Soil Biology and Biochemistry

Disruption of plant-soil-microbial relationships influences plant growth – Daniel P. Keymer – Journal of Ecology

Review: Rhizobial diversity and function in rooibos (Aspalathus linearis) and honeybush (Cyclopia spp.) plants: A review – C. Brink – South African Journal of Botany

Water and extremophile microbiome

Landscape-scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton – Juan Pablo Niño-García – Ecology Letters

Diversity and Distribution of Phenol Oxidase Producing Fungi from Soda Lake and Description of Curvularia lonarensis sp. nov. – Rahul Sharma – Frontiers in Microbiology

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

* Comparative study of Dushanzi and Baiyanggou mud volcano microbial communities in Junggar Basin in Xinjiang, China – Zhiyong Huang – International Research Journal of Public and Environmental Health

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Review: Sources of Antibiotics: Hot springs – Girish B. Mahajan – Biochemical Pharmacology

Metagenomics and bioinformatics

Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes – Jonsson Viktor – Journal of Computational Biology

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports

Techniques

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community – Miten Jain – Genome Biology

Microbes in the news

The “Internet Of Food,” DNA Testing, And The Quest For The Perfect Diet – Fastcompany

Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org

Major finding identifies nitrogen as key driver for gut health – Knowridge

Each animal species hosts a unique microbial community and benefits from it – David Salisbury – Vanderbilt University News

In Brazil, prestigious scientific journal “Nature Communications” focuses on Adventist lifestyle – Felipe Lemos – Adventist

Genes, early environment sculpt the gut microbiome – Science Daily

OpenBiome Now Stores Your Stool In Case of C. difficile Infection – Gastroenterology and Endoscopy News

November 29, 2016

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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

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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 26, 2016

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Human reproductive microbiome

Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk? – Kjersti Aagaard – EMBO Reports

Review: Female reproductive tract microbiome in gynecological health and problems – Shyamalina Haldar – Journal of Reproductive Health and Medicine

Animal microbiome

Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria – Violetta Vacchini – Environmental Microbiol Reports

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis – Juliane Wippler – BMC Genomics

Microbial communities of lycaenid butterflies do not correlate with larval diet – Melissa Whitaker – Frontiers in Microbiology

Bees: Report on the microbiota of Melipona quadrifasciata affected by a recurrent disease – Sebastián Díaz – Journal of Invertebrate Pathology

Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants – Aline Sartori Guidolin – Microbial Ecology

Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes – Dennis Versluis – Frontiers in Microbiology

Plant, root, and soil microbiome

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks – Eduardo Pérez-Valera –  Environmental Microbiology

Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System – Zhou Li – Environmental Microbiology

Water and extremophile microbiome

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano – Klaudia L. Hernández – Frontiers in Microbiology

Built environment / money microbiome

Dirty Money: A Matter of Bacterial Survival, Adherence, and Toxicity – Frank Vriesekoop – Microorganisms

Metabolomics

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes – Jeremy L. Motley – Journal of Natural Products

http://pubs.acs.org/doi/full/10.1021/acs.jnatprod.6b00772

Techniques

Note: human contamination in feces samples is usually low (e.g. compared to oral or vaginal samples; not really an issue in my opinion: An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction – Jitendra Kumar – Genomics, Proteomics & Bioinformatics

More microbiology

Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria – Fouad El Baidouri – Nature Ecology & Evolution

Press: Reshaping our ideas of bacterial evolution – Science Daily

Microbes in the news

This paper is not yet available online at Molecular Biology and Evolution, but already some press about it:
A comprehensive tree of prokaryotic life – Science Daily
New insights from the most comprehensive tree of prokaryotic life assembled to date – Phys.org

Bacteria taught to bond carbon and silicon for the first time – Aviva Rutkin – New Scientist

Binge-eating bacteria extract energy from sewage – Science Daily

Video: Good Germs; Bad Germs. Microbes in the kitchen, 14 households, 500 swabs – University of Oxford – YouTube

Bacteria Hysteria

Note: Sponsored by a company specialized in pest control and hygiene products. Primary school bacteria leaves teachers at risk of sickness – TES

November 25, 2016

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Human multisite microbiome (of dead bodies)

Thesis: Understanding the relationship between the human microbiome and urban decay/recovery among autopsied adults in Detroit, Michigan – Amanda T. Rzotkiewicz – Michigan State University

Human oral microbiome

The autoimmunity–oral microbiome connection – NG Nikitakis – Oral Diseases

Human reproductive and urinary tract microbiome

Potential contribution of the uterine microbiome in the development of endometrial cancer – Marina R. S. Walther-António – Genome Medicine

Proinflammatory Cytokines as Regulators of Vaginal Microbiota – E. A. Kremleva – Bulletin of Experimental Biology and Medicine

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Human gut microbiome

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Scientific Reports

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods – Andrew D. Huang – Applied and Environmental Microbiology

Review: Gut Microbiota and Autism: Key Concepts and Findings – Helen T. Din – Journal of Autism and Developmental Disorders

Review: Intestinal Microbiota as an Alternative Therapeutic Target for Epilepsy – Jiaying Wu – Canadian Journal of Infectious Diseases and Medical Microbiology

Review: Irritable Bowel Syndrome: A gut microbiota-related disorder? – Yogesh Bhattarai – American Journal of Physiology – Gastrointestinal and Liver Physiology

Review: Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities – Slyepchenko A. – Psychotherapy and Psychosomatics

Review: Microbiome, metabolites and host immunity – Maayan Levy – Current Opinion in Microbiology

Animal and in vitro models

* Persistent microbiome alterations modulate the rate of post-dieting weight regain – Christoph A. Thaiss – Nature

Press: Yo-yo weight gain driven by gut bacteria’s ‘memory’ of obesity, says study – Hannah Devlin – The Guardian
Breakthrough in Dieting Science: Gut Bacteria Are Behind Relapsing Obesity – Ido Efrati and Ruth Schuster – Haaretz

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition – Vitas E. Wagner – Science Translational Medicine

Antibiotics impair murine hematopoiesis by depleting intestinal microbiota – Kamilla S. Josefsdottir – Blood

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances – Wayne Young – Scientific Reports

Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat – Rosemarie De Weirdt – Environmental Microbiology

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits – Qiangchuan Hou – Scientific Reports

Evolutionary biologic changes of gut microbiota in an ‘adenoma-carcinoma sequence’ mouse colorectal cancer model induced by 1, 2-Dimethylhydrazine – Teng Sun – Oncotarget

Mini review: All Together Now: Experimental Multispecies Biofilm Model Systems – Chuan Hao Tan – Environmental Microbiology

Animal microbiome

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes – Hannes Horn – Frontiers in Microbiology

Plant, root, and soil microbiome

Soil Bacterial Community Response to Short-Term Manipulation of the Nitrogen Deposition Form and Dose in a Chinese Fir Plantation in Southern China – Caixia Liu – Water, Air, & Soil Pollution

Microbial community composition but not diversity changes along succession in arctic sand dunes – Anbu Poosakkannu – Environmental Microbiology

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles – Yang Li – Applied Microbiology and Biotechnology

Contrasting effects of two mammalian soil engineers on microbial communities – David J. Eldridge – Austral Ecology

* Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza – Hans Jacquemyn – Scientific Reports

 * Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids? – Stefania Cevallos – Mycorrhiza

Water and extremophile microbiome

Stromatolites from the Aptian Crato Formation, a hypersaline lake system in the Araripe Basin, northeastern Brazil – Lucas Veríssimo Warren – Facies

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River – Haohao Sun – Applied Microbiology and Biotechnology

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes – Carina Rofner – Global Change Biology

Viruses and phages

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture – Lavinia Gambelli – Frontiers in Microbiology

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Metabolomics

The role of metabolism (and the microbiome) in defining the clinical efficacy of dietary flavonoids – Aedín Cassidy – The American Journal of Clinical Nutrition

Metagenomics and bioinformatics

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports

Techniques

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities –
Anders Bjørnsgaard Aas – Molecular Ecology Resources

Microbes in the news

Stockholmers’ poop wanted in fight against drug-resistant bacteria – RT

The modern microbiome: Are we undoing evolution? – Maria Gloria Dominguez-Bello – ASM Cultures

PhD student finds surprising secret to detecting staph infections earlier – Breanne Grady – USC News

November 24, 2016

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Happy Thanksgiving! My inbox was full of exciting new papers, so here is a digest before I start cooking.

Microbiota and epigenetics, predatory bacteria to control infection, bacteria control water levels in leaves, microbial volatile compounds affect plant growth, the invertebrate virome, and natural products as mediators of disease.

Human respiratory microbiome

Evidence of microbiota dysbiosis in chronic rhinosinusitis – Michael Hoggard – International Journal of Allergy & Rhinology

Human gut microbiome

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins – Emily R. Davenport – BMC Genomics

New treatment options for irritable bowel syndrome with predominant diarrhea – Weber, H. Christian – Current Opinion in Endocrinology, Diabetes and Obesity

Animal models

* Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues – Kimberly A. Krautkramer – Molecular Cell

Press: Changes in the diet affect epigenetics via the microbiota – EurekAlert
Gut’s microbial community shown to influence host gene expression – EurekAlert

* Injections of Predatory Bacteria Work Alongside Host Immune Cells to Treat Shigella Infection in Zebrafish Larvae – Alexandra R. Willis – Current Biology

Harnessing the power of predatory bacteria as a ‘living antibiotic’ – Phys.org

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice – Tze Guan Tan – PNAS

Plant, root, and soil microbiome

+ Bacteria establish an aqueous living space in plants crucial for virulence – Xiu-Fang Xin – Nature

Press: Bacteria Spread Infection in Plants by Manipulating Water Level in Leaves – Howard Hughes Medical Institute

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus – Jonathan W. Leff – New Phytologist

Host species and environmental variation can influence rhizobial community composition
– Holly B. Vuong – Journal of Ecology

* Arabidopsis Responds to Alternaria alternata Volatiles by Triggering Plastid Phosphoglucose Isomerase-Independent Mechanisms – Ángela María Sánchez-López – Plant Physiology
* Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action – Ángela María Sánchez-López – Plant, Cell & Environment
* Commentary: The methylerythritol 4-phosphate pathway as a metabolic crossroad for microbial and plant volatile organic compounds – Manuel Rodriguez-Concepcion – Plant, Cell & Environment

Press: Compounds produced by phytopathogenic microbes encourage plant growth – EurekAlert

Water and extremophile microbiome

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers – Maggie C. Y. Lau – PNAS

Viruses and phages

* Redefining the invertebrate RNA virosphere – Mang Shi – Nature

World of viruses uncovered. Pioneering study of invertebrates discovers 1,445 viruses including several new families – EurekAlert

Metabolomics

* Review: Natural products as mediators of disease – Neha Garg – Natural Products Reports

Techniques

Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe – Sena Bae – PNAS

Research highlight: Culturomics: illuminating microbial dark matter – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Microbes in the news

Small world: The hot field of the microbiome. Ever since the discovery that bacteria can be good for us, there’s been a race to get into the lab. With Christine Szymanski and Josh Neufeld – Sharon Oosthoek – Maclean’s

Allergies: D-tryptophan explains probiotic characteristics of bacteria – Health Canal

Bacteria-destroying robot could replace antibiotics: Dutch inventer (sic) – Janene Pieters – NLTimes

Molecular chameleons reveal bacterial biofilm – EurekAlert

QIAGEN and CosmosID Launch New Plugin for Metagenomics Analysis – BusinessWire

Milliken recalls carpet cleaning powder on bacteria fears – Reuters

Bik’s non-microbiology Picks

Influence of Pokémon Go on Physical Activity: Study and Implications – Tim Althoff – arXiv

Aspartame may prevent, not promote, weight loss by blocking intestinal enzyme’s activity – EurekAlert