Category Archives: Human gut

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 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 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

November 23, 2016

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

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

Human gut microbiome

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

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

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

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

Microbiology of nearly sterile sites

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

Animal experiments

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

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

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

Water and extremophile microbiome

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

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

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

Food microbiology

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

Microbes in the news

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

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

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

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

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

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

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

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

November 22, 2016

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Vaginal Mirobiome in PPROM, Prevotella copri and rheumatoid arthritis, mice transplanted with stool from lean or obese humans, archaea in a pond.

Pregnancy and early life

High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study – Teenus Paramel Jayaprakash – PLOS ONE

Human oral microbiome

Review: The oral microbiome – an update for oral healthcare professionals – M. Kilian – British Dental Journal

Human gut microbiome

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis – C. Acharya – Alimentary Pharmacology and Therapeutics

In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children – Roberta Grimaldi – FEMS Microbial Ecology

Evidence for Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis – Annalisa Pianta – Arthitis & Rheumatology

Review: Human gut microbiota: the links with dementia development – Rashad Alkasir – Protein & Cell

Review: Gut hormones and gut microbiota: implications for kidney function and hypertensionGut hormones and gut microbiota: implications for kidney function and hypertension – Baris Afsar – Journal of the American Society of Hypertension

Review: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Interactions between gut microbes and host cells control gut barrier and metabolism – P D Cani – International Journal of Obesity Supplements

Review: Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – Oikos

Animal experiments

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans – Li Zhang – ISME Journal

Gut bacteria affect our metabolism – Science Daily

Animal microbiome

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae
– Shantanu P. Shukla – Molecular Ecology

Thesis: Characterization of the juvenile green turtle (Chelonia mydas) microbiome associated with the ontogenic shift from pelagic habitats to inshore resident areas – James T. Price – Purdue University

Tick microbiome and pathogen acquisition altered by host blood meal – Andrea Swei – The ISME Journal

Plant, root, and soil microbiome

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria – Natalia Pimentel Esposito-Polesi – Current Microbiology

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest – Witoon Purahong – Scientific Reports

High-methionine soybean has no adverse effect on functional diversity of rhizosphere microorganisms -J.G. Liang – Plant Soil Environment

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China – Jing Yan Tang – BMC Microbiology
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0892-3
Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons – Hirokazu Toju – PLOS ONE

Isolation and Identification of Keratinolytic Bacteria that Exhibit Feather-degrading Potentials – F. O. Iruolaje – Journal of Advances in Biology & Biotechnology

Water and extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis – Margarita Kambourova – Archaea

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities – Christine N. Shulse – Microbiology Open

Conference abstract: Defining the boarders of extreme life: The study of microbial communities and their settings gives insights into Mars analogue life within the MASE project – A Perras – 16th International Symposium on Microbial Ecology

Pollution microbiology

Influence of plantation on microbial community in porous concrete treating polluted surface water – Yan Long – International Biodeterioration & Biodegradation

Food microbiology

Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR – Cristiana Garofalo – International Journal of Food Microbiology

Viruses and phages

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments – Samuel L Diaz-Munoz – bioRxiv

More microbiology

Uncovering new drugs and targets – Andrea Du Toit – Nature Reviews Microbiology

Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Microbes in the news

‘Bacteria beaters’ win Longitude Prize Discovery Award – Shan Ross – The Scotsman

Bacteria for bio-toilets by February 15 – The Times of India

Your Office Has a Microbiome, and It Might Make You Sick – Zoe Schlanger – Wired

Tomato plants are more resistant against nematodes when colonized by a fungus – Farming Futures

Scientists use bacteria to map out NZ. A team of scientists growing bacteria in the shape of New Zealand have caught the attention of their colleagues across the globe – News Australia

The cover image is a map of New Zealand drawn with pyoverdine-producing P. aeruginosa cells in an ocean of indigoidine-synthesizing E. coli. – Cell Chemical Biology

Science, publishing, and career

Citizen science: The people behind the data – Mary Goodchild – NERC Planet Earth

November 21, 2016

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

Pregnancy and early life

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

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

Animal and in vitro experiments

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

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

Extremophile microbiome

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

Food microbiology

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

Metabolomics

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

Resistome

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

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

Microbes in the news

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

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

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

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

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