Category Archives: Extremophiles

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

November 15, 2016

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Microbial profiling in the classroom, viral abundance in seawater membrane vesicles, two Akkermansia in vitro studies, the phyllospere of Phoenix’ urban forest, the (im)possibility to reconstruct plasmids, high confidence protein annotations.

General microbiome

Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont – Lynn Chiu – PhilSci Archive

Microbial Community-Level Physiological Profiling as an Inquiry Laboratory Exercise – Pamela A. Marshall – The American Biology Teacher

Human oral microbiome

Bacterial communities associated with apical periodontitis and dental implant failure – Simon Dingsdag – Microbial Ecology in Health and Disease

Human respiratory microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff –  Current Opinion in Pulmonary Medicine

Human gut microbiome

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh – Shafiqul Alam Sarker – Environmental Microbiology

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery – Priscila Sala – Journal of International Medical Research

Review: The Human Microbiome and I-Cubed: A Modern Medical Paradigm – David S. Younger – World Journal of Neuroscience

Animal and in vitro models

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent – F. Van Herreweghen – Beneficial Microbes

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism – Renee L. Greer – Nature Communications

Animal microbiome

Black rhinoceros (Diceros bicornis) and domestic horse (Equus caballus) hindgut microflora demonstrate similar fermentation responses to grape seed extract supplementation in vitro – N. F. Huntley – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

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

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University

Diversity of phylloplane microflora in certain tea cultivars of Assam, North-East India – Amarjyoti Tanti – European Journal of Biological Research

Review: Do genetically modified plants affect adversely on soil microbial communities?
– Zheng-jun Guan – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology

Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches – Valerie F. Schwab – Biogeosciences

Trade-off between taxon diversity and functional diversity in European lake ecosystems – Lars Grossmann – Molecular Ecology

Glycerol enhances fungal germination at the water-activity limit for life – Andrew Stevenson – Environmental Microbiology

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India – Amrita Kumari Panda – AMB Express

Phages and viruses

Next-generation sequencing and norovirus – Matthew Cotten & Marion Koopmans – Future Virology

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates – Steven J Biller – ISME Journal

Metagenomics and bioinformatics

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data – Sergio Arredondo-Alonso – bioRxiv

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

Optimal prediction of the number of unseen species – Alon Orlitsky – PNAS

Constraint-based stoichiometric modelling from single organisms to microbial communities
– Willi Gottstein – Journal of the Royal Society Interface

Metabolomics, culturomics, proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns – Emma Timmins-Schiffman – The ISME Journal

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols – Max Crüsemann – Journal of Natural Products

Probiotics

Review: Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis – Jennifer McKean – The Journal of Alternative and Complementary Medicine

Microbes in the news

Good News at Fred Hutch: Evolutionary biologists Drs. Harmit Malik and Jesse Bloom win American Society for Microbiology awards – Fred Hutch

NTU don once downed a dish of live bacteria, for science’s sake – Straits Times

MCR-1 resistance gene could make its way into bacteria and superbugs in Australia – NT News
Biofilm battle is key to antibiotic war – University of Queensland

‘Probiotics’ on salad greens could make them safer, healthier – The University of Queensland

Monique Keiran: Laziness and hubris making us sick – Times Colonist

From the American Heart Association annual meeting: Could C-Section Birth Raise Child’s Risk of Obesity? – Dennis Thompson – Pantagraph

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 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 1, 2016

Posted on by

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 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

October 27, 2016

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Kavli Foundation grants, mycobiome of root canal infections, post-stroke infections,  Thai vegetarians, antibiotic treatment of gorillas, licorice plants under salt stress, and bacterial camouflage on Crustaceans. Greetings from New Mexico!

Jobs and grants

Open Positions at NC State University: Microbiomes and Complex Microbial Communities

Uniting Diverse Sciences to Tackle the Microbiome – Kavli Foundation

Human oral microbiome

The mycobiome of root canal infections is correlated to the bacteriome – Ilona F. Persoon – Clinical Oral Investigations

Near-sterile human body sites

Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method – the observation of DNAemia – T. Gosiewski – European Journal of Clinical Microbiology & Infectious Diseases

Human respiratory microbiome

Translocation and dissemination of commensal bacteria in post-stroke infection – Dragana Stanley – Nature Medicine

Bacteria in the respiratory tract—how to treat? Or do not treat? – Cristina Prat – International Journal of Infectious Diseases

Human gut microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study – Andrea Quagliariello – Nutrients

Review: Rethinking Diet to Aid Human–Microbe Symbiosis – Muriel Derrien – Trends in Microbiology

Review: Feeding the Microbiota-Gut-Brain Axis: Diet, Microbiome and Neuropsychiatry – Kiran V. Sandhu – Translational Research

Review: Microbiota dysbiosis: a new piece in the understanding of carcinogenesis puzzle – Valeria García-Castillo – Journal of Medical Microbiology

Review: The evolving role of the microbiome in liver failure and liver transplantation – Kymberly D. Watt – Liver Transplantation

Animal models

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla) – Klára Vlčková – Microbial Ecology

Commensal Microbe-specific Activation of B2 Cell Subsets Contributes to Atherosclerosis Development Independently of Lipid Metabolism – Lin Chen – EBioMedicine

Commentary: Intestinal Microbiome and Atherosclerosis – J. David Spence – EBioMedicine

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model – Susanne C. Diesner – Clinical Immunology

Kinetic changes of intestinal microbiota in the course of intestinal sensitization – Liang Xiao – Oncotarget

Animal microbiome

Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts – Gwynneth F. Matcher – Microbiology Open

Plant, root, and soil microbiome

Divergent responses of β-diversity among organism groups to a strong environmental gradient – Micael Jonsson – Ecosphere

Phylogenetic congruence between subtropical trees and their associated fungi – Xubing Liu – Ecology and Evolution

Microbial cooperation in the rhizosphere improves liquorice growth under salt stress – Dilfuza Egamberdieva – Bioengineered

Extremophile microbiome

Extremophiles: Life at the deep end – Sonja-Verena Albers – Nature

Built environment microbiome

Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital – Applied Microbiology and Biotechnology

Bioreactor microbiology

In vitro study of soil arsenic release by human gut microbiota and its intestinal absorption by Caco-2 cells – Naiyi Yin – Chemosphere

Probiotics

Probiotic With or Without Fiber Controls Body Fat Mass, Associated With Serum Zonulin, in Overweight and Obese Adults—Randomized Controlled Trial  – Lotta K. Stenman – EBioMedicine

More microbes

Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods – Laura E. Bagge – Current Biology

Press: Crustaceans in the ocean’s ‘twilight zone’ wear CAMOUFLAGE: Bacteria coating helps creatures avoid a predator’s gaze – Sarah Griffiths – Daily Mail

Microbes in the news

Videos from Microbiomes of the Built Environment NAS meeting posted – Jonathan Eisen – MicroBEnet

Iron-Loving Bacteria a Model For Mars Life – Elizabeth Howel –  Space.com

Dogs go on poop patrol to sniff out fecal bacteria. Rescue dogs trained to detect human fecal matter – Barbara Besteni – Local 10

Bacteria Sent In Space Could Be Potentially Infectious, Harmful – Elaine Hannah – Science World Report

Florida’s orange groves are being wiped out by tree-killing bacteria – CBS News

Rio fights Zika with biggest release yet of bacteria-infected mosquitoes. Wolbachia-infected mosquitoes will be widely deployed in two South American cities to combat viral infections – Ewen Callaway – Nature

Cranberries crush bacteria’s communication networks – Lisa-Ann Lee – New Atlas

Neonatal vaccination of mice with bacteria prevents cockroach-induced asthma as adults – News Medical

Bacteria and bugs in guts and gallbladders – Claire O’Connell – The Irish Times

October 25, 2016

Posted on by

Bat skin microbiome, carnivorous sponges, metagenome of an aquifer, and nitrogen fixation in symbionts of marine invertebrate animals.

Human respiratory microbiome

Microbial communities of conducting and respiratory zones of lung-transplanted patients – Marie Beaume – Frontiers in Microbiology

Animal microbiome

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

The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges – Jon T. Hestetun – Frontiers in Microbiology

Plant, root, and soil microbiome

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system – Karthik Anantharaman – Nature Communications

Press: New Bacteria Groups, and Stunning Diversity, Discovered Underground
Berkeley Lab and UC Berkeley research also provides new clues about the roles of subsurface microbes in globally important cycles– Dan Krotz – Berkeley Lab

Plant microbiomes and sustainable agriculture. Deciphering the plant microbiome and its role in nutrient supply and plant immunity has great potential to reduce the use of fertilizers and biocides in agriculture – Philip Hunter – EMBO Reports

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica – Sean T. S. Wei – Frontiers in Microbiology

Water microbiome

Seasonality of Coliform Bacteria Detection Rates in New Jersey Domestic Wells – Thomas B. Atherholt – Groundwater

Distinct factors shape aquatic and sedimentary microbial community structures in the lakes of western China – Jian Yang – Frontiers in Microbiology

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation – Jillian M. Petersen – Nature Microbiology

Press: ‘Farming’ bacteria to boost growth in the oceans – EurekAlert

Food microbiology

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

Proteomics

Proteomics of Microbial Human pathogens – Nelson C. Soares – Frontiers in Microbiology

Techniques

Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine – Yu-Hsin Hsieh – Frontiers in Microbiology

Microbes in the news

Google doodle honors van Leeuwenhoek, father of microbiology– Steven Musil – CNET

HT: Ian Brooks. Podcast: Microbes, Genes and Human Endeavour: Ed Yong seeks to expand our understanding of microscopic microbes – BBC

Call for submissions: Kavli microbiome ideas challenge – Joanna Urban – ASM

#BacteriaHysteria

Dogs Licking Humans Can Be Dangerous; Transmission of Bacteria, Viruses Possible – Nature World News