Category Archives: Plant Root Soil microbiome

November 12, 2016

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

General microbiome

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

Pregnancy and early life

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

Human respiratory microbiome

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

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

Human vaginal microbiome

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

Human esophagus and stomach microbiome

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

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

Human gut microbiome

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

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

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

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

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

Animal models

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

Water microbiome

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

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

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

Food microbiome

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

Probiotics

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

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

Viruses and phages

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

Metabolomics

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

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

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

More microbiology

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

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

Microbes in the news

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

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

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

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

 

 

November 10, 2016

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Fanconi anemia, Clostridium subcluster decreased in UC, ectomycorrhizas in oak forests, cryoconite hole anaerobes.

Human oral microbiome

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia – C.P. Furquim – Journal of Dental Research

Human gut microbiome

A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients – Kozue Takeshita – Inflammatory Bowel Diseases

Composition of gut microbiota in infants in China and global comparison – Ya-Shu Kuang – Scientific Reports

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease – Paul Giacomin – Scientific Reports

Making sense of the cause of Crohn’s – a new look at an old disease – Anthony W. Segal – F1000 Research

Metaanalysis: The Emerging Role of the Gut Microbiome in Adult Patients With Multiple Sclerosis – Pamela K. Newland – Journal of Neuroscience Nursing

Review: Escherichia coli Nissle 1917 in Ulcerative Colitis Treatment: Systematic Review and Meta-analysis – Giuseppe Losurdo – Journal of Gastrointestinal and Liver Diseases

Human blood and tissue microbiology

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections – Vibeke Børsholt Rudkjøbing – BMC Infectious Diseases

Review: Mechanisms of Bacterial Colonization of Implants and Host Response – Christof Wagner – Advances in Experimental Medicine and Biology

Animal models

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease – Ainsley M. Robinson – Inflammatory Bowel Diseases

Microbiota induces tonic CCL2 systemic levels that control pDC trafficking in steady state – M Swiecki – Mucosal Immunology

Siderophore-based immunization strategy to inhibit growth of enteric pathogens – Martina Sassone-Corsia – PNAS

Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice – Shaoqian Zhao – Journal of Molecular Endocrinology

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories – François-Joël Gatesoupe – BMC Microbiology

Plant, root, and soil microbiome

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition – Chengdong Huang – Field Crops Research

First detection of Endogone ectomycorrhizas in natural oak forests – Kohei Yamamoto – Mycorrhiza

[PFD] Grape berry bacterial inhibition by different copper fungicides – Guilherme Martins – BIO Web of Conferences

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Z Dai – Scientific Reports

Water and extremophile microbiome

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome – Marek K. Zdanowski – Microbial Ecology

Food microbiology

Sensory, microbiological and physico-chemical characterization of Klila, a traditional cheese made in the south-west of Algeria – Benamara R. N. – African Journal of MIcrobiology Research

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? – Bokai Zhu – Environment International

Built environment microbiology

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of MIcrobiology Research

Bioinformatics and metagenomics

Book chapter: DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data – Ilaria Granata – Dynamics of Mathematical Models in Biology

More microbiology

Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs – Kenneth Shatzkes – mBio

Predatory bacteria offer potential solution to drug resistance problem – Phys.org
Predatory Bacteria Can Cannibalize Drug-Resistant Bugs – Seeker

Bik’s non-microbiology Picks

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing – Mary A. Majumder – PLOS Biology

Origins of Biodiversity – Michael J. Benton – PLOS Biology

Microbes in the news

Researchers exploring new platform for detecting pathogenic bacteria using bacteriophages – News Medical

Novel vaccines block iron scavenging by bacteria. Agents starve bacteria by raising antibodies to capture the small molecules the microbes release to harvest iron – Stu Borman – Chemical & Engineering News

What’s lurking in the water in Shedd Aquarium – Lisa Bertagnoli – Chicago Business

New biophotonic light sensor can detect Legionella bacteria in minutes – News Medical

Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and the market

Clinical Microbiology Market Expected to Reach $6.72 billion by 2022 – Medgadget

Science, publishing, and career

Rosalind’s Ghost: Biology, Collaboration, and the Female – Caroline Wagner – PLOS Biology

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender – Xiao Han T. Zeng – PLOS Biology

November 9, 2016

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Today is a sad day. I’m in shock of last night’s results, and still sick at home, with only a small number of new papers in my Inbox.

Animal microbiome

Initial Characterization of the Pig Skin Bacteriome and Its Effect on In Vitro Models of Wound Healing – Matthew K. McIntyre – PLOS ONE

Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow trout Oncorhynchus mykiss from both farm and aquarium settings – Philip P. Lyons – Journal of Applied Microbiology

Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis – Soo Jin Jeon – PLOS ONE

Plant, root, and soil microbiome

Microbial Community Evolution Is Significantly Impacted by the Use of Calcium Isosaccharinic Acid as an Analogue for the Products of Alkaline Cellulose Degradation – Isaac A. Kyeremeh – PLOS ONE

Phages and viruses

Theory for the spatiotemporal interaction between lytic phages and biofilm-dwelling bacteria Theory for the spatiotemporal interaction between lytic phages and biofilm-dwelling bacteria – Matthew Simmons – bioRxiv

Microbes in the news

Quest to map Africa’s soil microbiome begins. Sub-Saharan project could one day help ecosystems to resist climate change and improve agricultureQuest to map Africa’s soil microbiome begins. Sub-Saharan project could one day help ecosystems to resist climate change and improve agriculture – Sarah Wild – Nature

Science, publishing, and career

Here’s some advice for you, President Trump, from scientists – Jeffrey Mervis – Science

Donald Trump’s US election win stuns scientists. Republicans sweep White House and US Congress, with uncertain implications for research – Jeff Tollefson, Lauren Morello& Sara Reardon – Nature

3 reasons researchers are terrified about Donald Trump’s presidency – Lindsay Dodgson – Business Insider

Scientists And Doctors Are Freaking Out About A President Trump – Virginia Hughes et al. – BuzzFeed

What the Trump win means for tech, science, and beyond. Net neutrality, science-based policy are threatened. A maximalist IP approach looms.– David Kravets – ArsTechnica

Microbiology Society announces new editor of Microbiology Today: Dr Rowena Jenkins from Cardiff Metropolitan University. Rowena’s term as Editor begins in January 2017

November 8, 2016

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I’m sick at home but my inbox is exploding with new papers, so I scraped myself together for a new Microbiome Digest.

Precision medicine and the microbiome, salivary microbiome of Tsimane mothers and infants, food emulsifiers promote colon cancer in mice, microplastics in urban rivers, and a hypothetical silver Nobel prize for Jeffrey Gordon.

Events

SF Bay Area Microbiome meetup – a new LinkedIn group for people in the San Francisco area interested in all things microbiome!

Society of Nutrition Education and Behavior (SNEB) Webinar – Probiotics: Understanding The Microbiome And The Role Of Probiotics In Long Term Health – Wednesday, December 7 at 12:00 p.m. EST

This one is about me: Stanford Microbiome Pioneer Elisabeth Bik Becomes New Science Editor at uBiome – uBiome

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz, Jack A. Gilbert – Trends in Pharmacological Sciences

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche – Sarah M. Kopac – Frontiers in Microbiology

Opinion: Do antibodies select a healthy microbiota? – Jason L. Kubinak & June L. Round – Nature Reviews Immunology

Editorial: Complexity at the sub-genus level – Andrea Du Toit – Nature Reviews Microbiology

Human oral microbiome

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication – Cliff S. Han – PeerJ

A Pilot Study to Evaluate the Oral Microbiome and Dental Health in Primary Open-Angle Glaucoma – Polla, Daniel – Journal of Glaucoma

Sputum microbiology predicts health status in COPD – DCW Braeken – International Journal of Chronic Obstructive Pulmonary Disease

Human respiratory microbiome

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases – Samuel M. Gonçalves – Virulence

Human vaginal microbiome

Effects of pelvic organ prolapse ring pessary therapy on intravaginal microbial flora – Kazuaki Yoshimura – International Urogynecology Journal

Review: Why do lactobacilli dominate the human vaginal microbiota? – SS Witkin – BJOG

Human gastric microbiome

Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status – Llorca, Laura – The Pediatric Infectious Disease Journal

Human gut microbiome

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome – Hailiang Xie – Cell Systems

Culture of previously uncultured members of the human gut microbiota by culturomics – Jean-Christophe Lagier – Nature Microbiology

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota – Francesco Miragoli – FEMS Microbiology Ecology

Animal models

Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
– Matthew B Biggs – The ISME Journal

Gut microbiota induce IGF-1 and promote bone formation and growth – Jing Yan – PNAS

Dietary emulsifier-induced low-grade inflammation promotes colon carcinogenesis – Emilie Viennois – Cancer Research

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth – Upsornsawan Itthitaetrakool – PLOS ONE

Sex-specific modulation of the gut microbiome and behavior in Siberian hamsters – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Animal microbiome

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates – Julie C. McInnes – Methods in Ecology and Evolution

High-throughput sequencing highlights the significant influence of seasonal housing and teat preparation on the raw milk microbiota – Conor J Doyle – Applied and Environmental Microbiology

Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves – Wei Li – Archives of Microbiology

Repeated sampling of white syndrome-affected corals reveals distinct microbiome at disease lesion fronts – F. Joseph Pollock – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest – Cheng Gao – New Phytologist

AMF, phylogeny, and succession: specificity of response to mycorrhizal fungi increases for late-successional plants – Liz Koziol – Ecosphere

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils – William A. Argiroff – Microbial Ecology

Effect of disturbance by oil pollution on the diversity and activity of bacterial communities in biological soil crusts from the Sultanate of Oman – Raeid M.M. Abed – Applied Soil Ecology

Book chapter: Root-Microbe Interactions in Response to Soil Conditions – Anil Somenahally – Global Soil Security

Water and extremophile microbiome

Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages – Amanda R. McCormick – Ecosphere

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii – Jason B. Sylvan – Geochimica et Cosmochimica Acta

Bacterial metacommunity organization in a highly-connected aquatic system – Silke Langenheder – FEMS Microbial Ecology

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland – Malin Bomberg – Biogeosciences

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia
– Shipeng Lu – Environmental Microbiology Reports

Review: Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook – Kela P. Weber – Water

Bioinformatics and metagenomics

Alternative for PiCRUST: Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes – Shoko Iwai – PLOS ONE

Measurement of bacterial replication rates in microbial communities – Christopher T Brown – Nature Biotechnology

Microbes in the news

If there was a Nobel silver medal, I’d award it to Jeffrey Gordon and our gut microbes – Tim Spector – The Conversation

The Microbiome Hits #1 for 2017: Cleveland Clinic’s announcement of the Top 10 Medical Innovations came at the conclusion of the 2016 Medical Innovation Summit.

Gut Instincts: The Link Between Diet, the Gut Microbiota and the Brain – Kiana West – Imperial College London

Q&A with Stanford statistics Professor Susan Holmes: Statistics in the era of big data – Stanford News

Conference report: Gut microbes linked to immunotherapy response in melanoma patients – EurekAlert

Gut bacteria ‘may help drugs fight cancer’ – James Gallagher – BBC

Assistant professor Joanna Slusky recognized for work with antibiotic-resistant bacteria – The University Daily Kansan

Three Soundcloud episodes by the Yale Journal of Biology and Medicine on the microbiome, to accompany their September issue:

  1. Microbiome: Episode I: history of the field, current techniques used in microbiome research, and how the microbiome influences our health
  2. Microbiome: Episode IIMicrobiome: Episode II: Dr. Martin Kriegel discusses articles published in our issue, – Yale Journal of Biology and Medicine
  3. Microbiome: Episode III: Dr. Camille Konopnicki, talks about current on going research on the microbiome here at Yale and how microbiome research is evolving and changing.

Companies Bet on Designer Bacteria as New Way to Treat Disease – MIT Technology Review

About Bethany Rader: Researcher studying squid-human bacteria connection – Tim Crosby – The Southern Illinoisan

Horrible title, but nice student work: Students create Frankenstein’s monster of bacteria to detect toxic chemicals – New Atlas

 

November 7, 2015

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Colon cancer tumor location and Fusobacterium nucleatum abundance, eczema in infants, fungi in Crohn’s disease, pH 4 in Yellowstone.

Pregnancy and early life

Altered Gut Microbiota Composition Associated with Eczema in Infants – Huajun Zheng – PLOS ONE

Predominant Lactobacillus species types of vaginal microbiota in pregnant Korean women: quantification of the five Lactobacillus species and two anaerobes – Jeong Hyun Kim – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis – An Hotterbeekx – Scientific Reports

Human gut microbiome

Fungal Microbiota Profile in Newly-diagnosed Treatment-naïve Children with Crohn disease – Mohammad El Mouzan – Journal of Crohn’s and Colitis

Analysis of the Duodenal Microbiome in Autistic Individuals: Association with Carbohydrate Digestion – Kushak, Rafail I. – Journal of Pediatric Gastroenterology and Nutrition

Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location – Kosuke Mima – Clinical and Translational Gastroenterology

Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkinsonism & Related Disorders

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota  – Francesco Miragoli – FEMS Microbiology Ecology

Title is confusing; “No change in mucosal gut Mycobiome” would have been more clear. No Change in the Mucosal Gut Microbiome is Associated With Celiac Disease-Specific Microbiome Alteration in Adult Patients – Valeria D’Argenio – American Journal of Gastroenterology

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: Role of vitamin D on gut microbiota in cystic fibrosis – Mansi Kanhere – The Journal of Steroid Biochemistry and Molecular Biology

Review: Nutrition and the Gut Microbiome in the Elderly – Nuria Salazar – Gut Microbes

Addendum: Support for the Microgenderome Invites Enquiry into Sex Differences – Amy Wallis – Gut Microbes

Animal models

Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model – R. Alan Harris – Scientific Reports

Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Animal microbiome

Identifying bacterial predictors of honey bee health – Giles E. Budge – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios – Enrico Tatti – Applied Soil Ecology

Bacterial and fungal community structure and diversity in a mining region under long-term metal exposure revealed by metagenomics sequencing – Ramya Narendrula-Kotha – Ecological Genetics and Genomics

Conversion of grassland to arable decreases microbial diversity and alters community composition – Katherine E. French – Applied Soil Ecology

Water and extremophile microbiome

Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains – Guang Li Yan – Scientific Reports

Microbial community analysis of pH 4 thermal springs in Yellowstone National Park – Xiaoben Jiang – Extremophiles

Food microbiology

Microbiota of high-pressure-processed Serrano ham investigated by culture-dependent and culture-independent methods – N. Martínez-Onandia – International Journal of Food Microbiology

Applicability of commercial phage-based products against Listeria monocytogenes for improvement of food safety in Spanish dry-cured ham and food contact surfaces – Diana Gutiérrez – Food Control

Pollution and waste microbiology

Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production – Nachiket P. Marathe – PLOS ONE

Microbes in the news

Costa Rican ants might have the secret to better antibiotics – L. Arias – TicoTimes

Waterfowl Worry: Recurring disease kills loons, other birds – Washington Times

STEM Gets Marvelous for a Local Student – how the microbes on the scalp could impact the hair growth – NCTV17.com

Best-selling cleanser recalled over dangerous levels of bacteria. Liz Earle’s ‘Cleanse & Polish Hot Cloth Cleanser’ found to contain potentially dangerous bacteria – Ben Kentish – Interdependent

Microbes and the market

APC Microbiome Institute: Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Financial Times

November 4, 2016

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A very short Digest today, since Stanford unexpectedly closed my email account, so I cannot access most eTOCs. I had requested a couple of months extension, but it did not happen 😦   Here is what I found for you today:

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’ – Tess E. Brewer – Nature Microbiology

Mycorrhizal compatibility and symbiotic seed germination of orchids from the Coastal Range and Andes in south central Chile – Hector Herrera – Mycorrhiza

Microbes in the news

One of our reporters tried to do CRISPR. He failed miserably – Jon Cohen – Science

Polysorbate as possible E. coli food poisoning fix – Barfblog

Food Additive Could Treat E. Coli Food Poisoning – ValueWalk

A penguin in the Bombay Zoo that recently died: Dory’s death: one more test confirms bacterial infection – Tanvi Deshpande
Finding Dory’s killer? Authorities in no rush – Rupsa Chakraborty – Midday

Microbes on the market

OptiBiotix Health Plc Presentation of data at European Microbiome Summit – Directors Talk Interviews

Enterome Appoints Christophe Bonny as Chief Scientific Officer – PR Newswire

#BacteriaHysteria

The dirt on phones: See what you’re holding in your hands – WIBW

 

 

November 3, 2016

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Prevotella and Bacteroides associations with diet, parasite-microbiota interactions in wild animals, Staphylococcus/fungus interactions in cheese rind.

General microbiome

The Underestimation of Global Microbial Diversity– Jay T. Lennon -mBio

Next-Generation High-Throughput Functional Annotation of Microbial GenomesNext-Generation High-Throughput Functional Annotation of Microbial Genomes – Ralph S. Baric – mBIo

Human vaginal microbiome

The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next? – Anita Mitra – Microbiome

Human gut microbiome

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns – Francesca De Filippis – Microbiome

(PubMed link) Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohn’s Disease – Dunn KA – Inflammatory Bowel Diseases

(PubMed link) Review: The role of the gut microbiota in food allergy – Rachid R – Curr Opin Pediatr

Review: Intestinal Microbiome Changes and Stem Cell Transplantation: Lessons Learned – Ying Taur – Virulence

Human urinary tract microbiome

Review: Urinary Tract Infection: Pathogenesis and Outlook – Lisa K. McLellan – Trends in Molecular Medicine

Animal microbiome

Parasite-microbiota interactions potentially affect intestinal communities in wild mammals – Tuomas Aivelo – bioRxiv

Plant, root, and soil microbiome

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator – J. L. Wood – Scientific Reports

Food microbiology

Cheese: Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species – Erik K. Kastman – mBio

Press: Fungi boost bacterium. A study of 25 cheeses finds that a slow-growing bacterium can outcompete its relatives with the help of fungi – Nature

Storage techniques

Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies – Erikka Loftfield – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Why Gut Bacteria Are Having a Moment. Jessica Richman, CEO of uBiome at Fortune’s Brainstorm Health summit- Beth Kowitt – Fortune

The Life, the Sea and the Space Viking, Searching for Extremophiles – Seti

Are You Ready to Swallow a Pill Full of Poop? OpenBiome believes in the power of pure, barely processed poop – Katie M. Palmer – Wired

Gut microbiome profiles predict response to low FODMAP diet in IBS – Healio

Study links intestinal microbial population to production of inflammatory proteins – Economic TImes

Guts of Fecal Transplant Patients Resemble their Donors’ – HCP Live – Refers to this paper: http://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-016-0698-z

Microbiome Skincare: Is Bacteria the Key to Perfect Skin? A primer on the science that could fix our skin woes once and for all – Wing Sze Tang – Flare

November 1, 2016

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Ribosomal gene sequencing as a clinical diagnostic tool, probiotic microcins in the inflamed gut, toxic sugar metabolism by a bee symbiont, bacteria as indicators of soil condition, viruses of the human body.

General microbiome

Omics Approaches To Probe Microbiota and Drug Metabolism Interactions – Robert G. Nichols – Chemical Research in Toxicology

Review: Microbial interactions: ecology in a molecular perspective – Raíssa Mesquita Braga – Brazilian Journal of Microbiology

Human skin microbiome

Understanding the role of Propionibacterium acnes in acne vulgaris: the critical importance of skin sampling methodologies – Hélène Omer – Clinics in Dermatology

Human respiratory microbiome

Editorial: Macrolides, inflammation and the lung microbiome: untangling the web of causality – Robert P Dickson – Thorax

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Emerging pathogenic links between microbiota and the gut–lung axis
– Kurtis F. Budden – Nature Reviews Microbiology

Human gut microbiome

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions – Daniel E Almonacid – bioRxiv

Detecting beer intake by unique metabolite patterns – Gözde Gürdeniz – Journal of Proteome Research

Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

The infant gut microbiome correlates significantly with rotavirus vaccine response in rural Ghana – Vanessa C. Harris – Journal of Infectious Diseases
Could the gut microbiome be key to understanding and improving rotavirus vaccine performance in high disease burden settings? – Journal of Infectious Diseases

Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors – M L Stoll – Genes and Immunity

Can the composition of the intestinal microbiota predict the development of urinary tract infections? – Casper DJ den Heijer – Future Microbiology

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Good Bugs, Bad Bugs in the Gut: The Role of Microbiota Dysbiosis in Chronic Gastrointestinal Consequences of Infection – Andre G Buret – American Journal of Gastroenterology

Review: Soy and Gut Microbiota: Interaction and Implication for Human Health – H Huang – J Agric Food Chem

Review: The gut microbiome and hypertension – M Pevsner-Fisher

Probiotics

Microcins mediate competition among Enterobacteriaceae in the inflamed gut – Martina Sassone-Corsi – Nature

Press: How good gut bacteria wrest control from the bad – Cosmos Magazine

Novel encapsulation improves recovery of probiotic strains in fecal samples of human volunteers – Volker Mai – Applied Microbiology and Biotechnology

Psychobiotics and the Manipulation of Bacteria–Gut–Brain Signals – Amar Sarkar – Trends in Neurosciences

Press: Psychobiotics: What Do We Know and Where Do We Go? – Laurie Anne Walden – Contagion Live

Review: Eosinophils, probiotics, and the microbiome – Helene F. Rosenberg – Journal of Leukocyte Biology

Animal experiments

Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice – Jing-jing Wang – Scientific Reports

Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

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

Animal microbiome

Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicola – Hao Zheng – mBio

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites – Aram Mikaelyan – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacteria as emerging indicators of soil condition – Syrie M. Hermans – Applied and Environmental Microbiology

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens – Longfei Jiang – Scientific Reports

Endophytic Bacillus cereus effectively controls Meloidogyne incognita on tomato plants through rapid rhizosphere occupation and repellent action – Haijing Hu – Plant Disease

Drivers of yeast community composition in the litter and soil of a temperate forest –
Tereza Mašínová – FEMS Microbiology Ecology

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat – Michele Perazzolli – BMC Genomics

The root growth of wheat plants, the water conservation and fertility status of sandy soils influenced by plant growth promoting rhizobacteria – Naeem Khan – Symbiosis

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices – Jae-Hyung Ahn – Journal of Microbiology

Partitioning the effect of composition and diversity of tree communities on leaf litter decomposition and soil respiration – Mark Davidson Jewell – Oikos

Effects of Land use on the Structural Diversity of Soil Bacterial Communities in South Eastern Iran – Ghobad Jalali – Biosciences Biotechnology Research

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Antarctic strict anaerobic microbiota from Deschampsia antarctica vascular plants rhizosphere reveals high ecology and biotechnology relevance – Rafael José Marques Peixoto – Extremophiles

The influence of the host plant is the major ecological determinant of soil presence of the nitrogen-fixing root nodule symbiont, Cluster II Frankia – Kai Battenberg – Applied and Environmental Microbiology

Review: Fungal endophytes and their interactions with plants in phytoremediation: A review – Zujun Deng – Chemosphere

Water and extremophile microbiome

Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the north Atlantic ocean – Elisa Guerrero-Feijóo

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products – Miguel David Marfil-Santana – Journal of Microbiology

Food microbiology

Different flour microbial communities drive to sourdoughs characterized by diverse bacterial strains and free amino acid profiles – Giuseppe Celano – Frontiers in Microbiology

Built environment microbiome

Drinking water: One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria – Antonia Bruno – Microbiology Open

Weathering of a Roman Mosaic—A Biological and Quantitative Study on In Vitro Colonization of Calcareous Tesserae by Phototrophic Microorganisms – Addolorata Marasco – PLOS ONE

Bioinformatics and metagenomics

Phylogenetic Dirichlet-multinomial model for microbiome data – Yunfan Tang – arXiv

More microbiology

Bacterial evolution: Genomics of metabolic trade-offs – Martin F. Polz – Nature Microbiology

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences – Huimin Zhang – Molecular Biotechnology

Review: A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Viruses of the Human Body. Some of our resident viruses may be beneficial – Eric Delwart – The Scientist

Naval Special Warfare Trainees Face Tiny Enemy: Bacteria – Sara G. Miller – Live Science

Could a disrupted sleep also disturb your gut? – Fiona Pepper for The Health Report

Researchers think they’ve finally figured out why bacteria only causes acne in some people. And how to stop it. – Fiona MacDonald – Science Alert

Microbes and the market

uBiome CEO Jessica Richman Joins Sean Parker, Maria Shriver, Arianna Huffington and Others, Speaking at Fortune Brainstorm HEALTH

Science, publishing, and career

2016 Life Sciences Salary Survey. Most researchers feel stimulated by their work but are dissatisfied with their compensation, according to this year’s results – Karen Zusi – The Scientist

October 31, 2016

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Happy Halloween! Today is the first day at my new employer uBiome. But the blog continues. Today’s blog features the gut microbiome of Type 2 Diabetes patients and the transportome of mycorrhiza.

Human skin microbiome

Inhibition of HDAC8 and HDAC9 by microbial short-chain fatty acids breaks immune tolerance of the epidermis to TLR ligands – James A. Sanford – Science Immunology

Press: Acne Gives Up Secret That Points to New Treatments – Amy Norton – WebMD

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Animal microbiome

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome – Lizi Bensoussan – Environmental Microbiology

Plant, root, and soil microbiome

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza – Kevin Garcia – Trends in Plant Science

Microbes in the news

Bacteria, other contaminants make costume contact lenses risky – NBC

Nurses’ Scrubs Carry Bad Bacteria. Healthcare workers, patients, and environment form ‘transmission triangle’ – Liz Highleyman – MedPage Today

A Word from Dr. Pfenninger: The weird disease of tetanus – John L. Pfenninger – Midland Daily News

Doctors transfer the power of gut bacteria – Emery Cowan – AZ Daily Sun

October 29, 2016

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Laryngeal microbiome, nitrogen fixation by bivalve symbionts, subalpine snow in California, sequence data compression tools. Flying back to Cali today, blogging from Phoenix.

Human respiratory microbiome

The human laryngeal microbiome: effects of cigarette smoke and reflux – Marie E. Jetté – Scientific Reports

Animal microbiome

This is pretty cool: Nitrogen fixation in a chemoautotrophic lucinid symbiosis – Sten König – Nature Microbiology

Fecal Bacterial Composition of Sichuan Snub-Nosed Monkeys (Rhinopithecus roxellana) – Chen Su – International Journal of Primatology

Lesion recovery and the bacterial microbiome in two Caribbean gorgonian corals – Kartick P. Shirur – Marine Biology

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth-Promoting Rhizobacteria (PGPR) from the Rhizosphere of Sugarcane in Saline and Non-Saline Soil – Elham Lamizadeh – International Journal of Current Microbiology and Applied Science

Different responses of rhizosphere and non-rhizosphere soil microbial communities to consecutive Piper nigrum L. monoculture – Zhigang Li – Scientific Reports

Note: 16S rRNA amplicon study, not metagenomics. Proceed with caution. Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data – José R. Valverde – PLOS ONE

Comparison of Microbial Community Composition and Diversity in Native Coastal Wetlands and Wetlands that Have Undergone Long-Term Agricultural Reclamation – Shiqi Xu – Wetlands

Review: Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics – Laurent Kamel – New Phytologist

Review: Plant microbiomes and sustainable agriculture – Philip Hunter – EMBO press

Water and extremophile microbiome

Microbial community structure of subalpine snow in the Sierra Nevada, California – Chelsea J. Carey – Arctic, Antarctic, and Alpine Research

Unique community structure of viruses in a glacier soil of the Tianshan Mountains, China – Li-Li Han – Journal of Soils and Sediments

Composition and distribution of microbial communities in natural river wetlands and corresponding constructed wetlands – Qingqing Ca – Ecological Engineering

The culturable mycobiota of a Mediterranean marine site after an oil spill: Isolation, identification and potential application in bioremediation – Elena Bovio – Science of the Total Environment

Metagenomics and bioinformatics

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes – Daniel R. Mende – Nucleic Acids Research

Comparison of high-throughput sequencing data compression tools – Ibrahim Numanagić – Nature Methods

Phages and ecology

Ecological conditions determine extinction risk in co-evolving bacteria-phagepopulations – Rosanna C. T. Wright – BMC Evolutionary Biology

Microbes in the news

‘Rare’ and ‘unusual’ bacteria discovered on Muni by SFSU researchers – Alyssa Pereira – SF Gate

How lack of oxygen makes bacteria cause acne and how to stop it – Andy Coghlan – New Scientist

Necrotizing Fasciitis: A Profound Mystery In Medical Microbiology – Alex Berezow – American Council on Science and Health

Doctors warn of bacteria in salt water after Jacksonville officer almost dies – Letisha Bereola – Action News Jax

Healdsburg company makes ‘food’ for the gut’s bacteria – Press Democrat