Category Archives: Human gut

August 11, 2015

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Several reviews on human gut microbiome, two papers on coral microbiome, gut microbiota of wild mice, ancient sea microbes found in gold mine stalactites, and an update on the tree of life.

Microbiome of Death

Not a microbiota paper, but cannot leave out: A Longitudinal Study on Human Outdoor Decomposition in Central Texas – Joanna K. Suckling – Journal of Forensic Sciences

Human gut microbiome

Anti-tumour Necrosis Factor Treatment with Adalimumab Induces Changes in the Microbiota of Crohn’s Disease – David Busquets – Journal of Crohn’s and Colitis

Reduced Levels of D-dimer and Changes in Gut Microbiota Composition after Probiotic Intervention in HIV-infected Individuals on Stable ART – Birgitte Stiksrud – Journal of Acquired Immune Deficiency Syndromes

The human gut microbiome as a transporter of antibiotic resistance genes between continents – Johan Bengtsson-Palme – Antimicrobial Agents and Chemotherapy

Review: The gut microbiota in human energy homeostasis and obesity – Michael Rosenbaum – Trends in Endocrinology & Metabolism

Review: Understanding probiotics’ role in allergic children: the clue of gut microbiota profiling – Pamela Vernocchi – Current Opinion in Allergy and Clinical Immunology

Editorial: The Role of Bacteria in Necrotizing Enterocolitis: Understanding the Forest for the Trees – McElroy S.J – Neonatology

Review: Implications of microbiota and bile acid in liver injury and regeneration – Hui-Xin Liu – Journal of Hepatology

Animal and bioreactor models

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin – Lindsey Chambers – PLOS ONE

Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces – Li Li – Journal of Food Science

Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy – Raphael Barbetta de Jesus – Acta Scientiarum

Animal microbiome

The Gut Microbiota of Wild Mice – Laura Weldon – PLOS ONE

Necrotizing Enterocolitis in Preterm Pigs Is Associated with Increased Density of Intestinal Mucosa-Associated Bacteria Including Clostridium perfringens – Støy A.C.F. – Neonatology

Cecal drop reflects the chickens’ cecal microbiome, fecal drop does not – J. Pauwels – Journal of Microbiological Methods

Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals – Marie La Rivière – Coral Reefs

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral – Sarah A. Gignoux-Wolfsohn – PLOS ONE

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – J. Hubert – Journal of Applied Microbiology

Plant, root, and soil microbiome

Remediation of diesel-contaminated soil using in situ chemical oxidation (ISCO) and the effects of common oxidants on the indigenous microbial community: a comparison study – Ku-Fan Chen – Journal of Applied Microbiology

Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition – An Yang – Frontiers in Microbiology

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans – Anish Bhattacharyya – Archaea

Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil – Sammy Frenk – FEMS Microbial Ecology

Effects of biochar on copper immobilization and soil microbial communities in a metal-contaminated soil – Sebastián Meier – Journal of Soils and Sediments

Factors associated with the diversification of the microbial communities within different natural and artificial saline environments – Shilong He – Ecological Engineering

Review: Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? – Aimée T. Classen – Ecosphere

Water microbiome

Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas – Gaëtan Borgonie – Frontiers in Microbiology

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments – Haoxin Fan – Frontiers in Microbiology

Waste treatment microbiology

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor – Zhang Bin – Scientific Reports

Proteomics

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data – Laurence Yang – PNAS

Colonic metaproteomic signatures of active bacteria and the host in obesity – Carolin A. Kolmeder – Proteomics

More microbes

The universal tree of life: an update – Patrick Forterre – Frontiers in Microbiology

How Do Microbial Populations and Communities Function as Model Systems? – Maureen O’Malley – The Quarterly Review of Biology

Impact of space flight on bacterial virulence and antibiotic susceptibility – Peter William Taylor – Infection and Drug Resistance

Microbes in the news

Look Up! There’s an Invisible Zombie Highway Right Above You – Robert Krulwich – National Geographic

uBiome Invites Health Care Providers to Join New Clinical Microbiome Consortium – Global News Wire

Our microbiome: Separating hype from health – Nicholas Staropoli – Genetic Literacy Project

Poop Transplants And Microbiome Makeovers: How We’ll Engineer Our Bacteria To Feel Better – Jessica Leber – FastCoExist

Researchers Offer New Insights Into the Pulmonary Microbiota of Cystic Fibrosis Patients – Patricia Silva – Cystic Fibrosis News Today

Conflict and Co-operation in Bacterial Communities – MicrobePost

Can Your Body’s Bacteria Cause Cancer? – Charis Eng – Cleveland Clinic

British Ministry of Defense released potentially lethal bacteria on London Tube (in 1963), chemically experimented on soldiers – Russell Boyce – RT

Engineered Bacteria Send A Signal When Water Gets Polluted – Tracy Staedter – Discovery

JGI to Grant $1.2 Million to Genomic Technology Projects – Genome Web

Science, publishing, and career

Science: The Story of Me – Morgan Pak – Huffington Post

4 Ways to Help Everyone Find Their Inner Scientist – Imogen Coe – Huffington Post

Tech Women in India’s Startup Boom Reach Out – Gagandeep Kaur – WomensEnews

Bik’s Picks

Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans – Andrés Vidal-Gadea – eLIFE

Here’s why coffee makes you poop – Rachel Feltman – Washington Post

Why You’re More Likely To Be Killed By a Bee Than a Bear: Our fear of bear attacks is far greater than the actual risk of being mauled or killed, experts say. – Carrie Arnold – National Geographic

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August 8, 2015

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Lung and oral microbiomes in setting of HIV infection, cell biology of the plant–microbe interface, deep see prokaryotes, bacterial succession during grape fermentation, and correcting amplicon errors with Dada2.

Pregnancy and birth microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Multiple Opportunistic Pathogens, but Not Pre-existing Inflammation, May Be Associated with Necrotizing Enterocolitis – Steven T. Leach – Digestive Diseases and Sciences

Review: Nutrient availability, the microbiome and intestinal transport during pregnancy – Stuart Astbury – Applied Physiology, Nutrition, and Metabolism

Human oral and lung microbiome

Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals – James M. Beck – American Journal of Respiratory and Critical Care Medicine

Review: Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis – Frank A. Roberts and Richard P. Darveau – Periodontology 2000

Needs assessment for emerging oral microbiome knowledge in dental hygiene education – R. Constance Wiener – Journal of Epidemiological Research

Human reproductive microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Human gut microbiome

Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid – Jayakanthan Kabeerdoss – Indian J Med Res

An In Vitro Method to Assess Soil Arsenic Metabolism by Human Gut Microbiota: Arsenic Speciation and Distribution – Naiyi Yin – Environmental Science & Technology

Review: Does a low FODMAP diet help IBS? – Drug and Therapeutics Bulletin

Microbiome models

Modulation of intestinal microbiota in mice by kefir administration – Dong-Hyeon Kim – Food Science and Biotechnology

High nutrient availability reduces the diversity and stability of the equine caecal microbiota – Naja C. K. Hansen – Microbial Ecology in Health & Disease

Impact of Dietary Fiber/Starch Ratio in Shaping Cecal Microbiota in Rabbits – YanLi Zhu – Canadian Journal of Microbiology

Animal microbiome

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode – Sumihiro Koyama – Marine Biotechnology

PhD Thesis: Reproduction, Sex Ratio and Bacterial Communities of the Coffee Berry Borer Hypothenemus Hampei F. (Coleoptera: Curculionidae) – Mariño Cárdenas – Universidad de Puerto Rico

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro – Brittany E. Harlow – Journal of Applied Microbiology

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish – V. V. Kuz’mina – Fish Physiology and Biochemistry

Plant, root, and soil microbiome

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities – Weibing Xun – Soil Biology and Biochemistry

Editorial: Introduction to a Virtual Special Issue on cell biology at the plant–microbe interface – Ralph Panstruga and Hannah Kuhn – New Phytologist

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China – Jing Zhou – Soil Biology and Biochemistry

Functional and structural responses of methanogenic microbial communities in Uruguayan soils to intermittent drainage – Yang Ji – Soil Biology and Biochemistry

Effects of pasture management on soil fertility and microbial communities in the semi-arid grasslands of Inner Mongolia – Jun Liu – Journal of Soils and Sediments

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs – Alessio Mengoni – Research in Microbiology

Effect of combined microbes on plant tolerance to Zn–Pb contaminations – Anna Ogar – Environmental Science and Pollution Research

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples – Weimin Sun – Applied Microbiology and Biotechnology

Water microbiome

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites – Aurélien Saghaï – Frontiers in Microbiology

Thesis: Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA – Jacob Preston Beam – Montana State University

Global diversity and biogeography of deep-sea pelagic prokaryotes – Guillem Salazar – ISME Journal

Built environment microbiology

Halophilic microbial communities in deteriorated buildings – Justyna Adamiak – World Journal of Microbiology and Biotechnology

Food microbiology

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes – Hailan Piao – Frontiers in Microbiology

Identification of key microorganisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation – Chen Chen – Journal of Applied Microbiology

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output – Patricia Gullón – Food & Function

Bioinformatics

DADA2: High resolution sample inference from amplicon data – Benjamin J Callahan

Transcriptomics

Molecular and chemical dialogues in bacteria-protozoa interactions – Chunxu Song – Scientific Reports

Techniques

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE

Microbes in the News

Prestigious Japanese university comes up with cheesecake … made with Gorilla bacteria! – RocketNews

Lambton College research project proves successful in eliminating bacteria in firefighting gear – Lambton College

Where the sausage gets made – Holly Ganz – MicroBEnet

Calgary diseases expert on the importance of studying our guts – The Globe and Mail

Bik’s Picks

Creepers’ peepers: Why animals’ pupils have different shapes – Nicholas St. Fleur – Seattle Times

Venomous frogs discovered during painful scientific mishap: Frogs head-butt enemies with their spines to inject toxic venom – CBC News

ISS Astronauts to Sample Leafy Greens Grown on Space Station – NDTV

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August 6, 2015

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Obesity in Korean adolescents, banana rhizosphere, rare taxa and Deepwater Horizon spill, leaking septic tanks, and visualization of ‘omics data.

Events

BioMicroWorld 2015: International Conference on Environmental, Industrial and Applied Microbiology, 28-30 October 2015, Barcelona, Spain – Has a workshop called: “Modelling bacterial dynamics using the R software”

Human oral and gut microbiome

Oral and faecal microbiota in volunteers with hypertension in a double blind, randomised placebo controlled trial with probiotics and fermented bilberries – Jie Xu – Journal of Functional Foods

Obesity Alters the Microbial Community Profile in Korean Adolescents – Hae-Jin Hu – PLOS ONE

Microbiome models

Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity – Blanda Di Luccia – PLOS ONE

Plants, roots, and soil microbiome

Manipulating the banana rhizosphere microbiome for biological control of Panama disease – Chao Xue – Scientific Reports

Review: Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity – Barbara Reinhold-Hurek – Annual Review of Phytopathology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Effect of genetically modified rice producing resveratrol on the soil microbial communities – Soo-In Sohn – Journal of the Korean Society for Applied Biological Chemistry

Water microbiome

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume – Sara Kleindienst – The ISME Journal

Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale – Marc P. Verhougstraete – PNAS

Toolbox approaches using molecular markers and 16S rDNA amplicon datasets for the identification of fecal pollution in surface water – W. Ahmed – Applied and Environmental Microbiology

Bioinformatics

Anvi’o: An advanced analysis and visualization platform for ‘omics data – A. Murat Eren – Peer J

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads – Binbin Lai – BMC Bioinformatics

MiRKAT peeks at associations between the microbiome and disease – —JM Kocarnik – Fred Hutch

Fungi and microbiomes

Noisy neighbourhoods: quorum sensing in fungal polymicrobial infections – Emily F. Dixon – Cellular Microbiology

Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences – Adrian Langarica-Fuentes – Microbiology

More microbes

Review: Next-generation sequencing for pathogen detection and identification – Kenneth G. Frey – Methods in Microbiology

Microbes in the news

University of Missouri hosts open house at DNA sequencing center – Megan Favignano – Columbia Tribune

Detective work traces bacteria in Michigan rivers back to leaky septic tanks – Rebecca Williams – Michigan Radio

Bacteria that may cause spotty liver disease in chickens identified – Farmers Weekly

Bik’s Picks

World’s first ant map launched in Hong Kong:geographic locations of nearly 15,000 types of ant – Business Insider

Seeds That Defied Romans, Pirates, and Nazis – Robert Krulwich – National Geographic

The dark side of the moon sails across Earth in new NASA video – Deborah Netburn – Los Angeles Times

 

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August 5, 2015

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Microbiome in patients with Irritable Bowel Syndrome, gastric bypass operations induces long-term microbiome changes, environmental enteropathy in a mouse model, respiratory viruses in large families, and microbiology of restaurant grease waste.

Events

Microbiome R&D and Business Collaboration Forum – September 10-11, 2015, San Diego, USA

European Microbiome Congress 2015 – 18 and 19 November 2015, London, UK

Microbiome of pregnancy and birth

Review: Antibiotics and the developing infant gut microbiota and resistome – Molly K Gibson – Current Opinion in Microbiology

Review: Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System – Cong, Xiaomei – Advances in Neonatal Care

Review: The Prescient Placenta – Christopher Coe – The Scientist

Human respiratory microbiome

Community Surveillance of Respiratory Viruses Among Families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) Study –  L. Byington – Clinical Infectious Diseases

Human gut microbiome

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome – Marta Pozuelo – Scientific Reports

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation – Valentina Tremaroli – Cell Metabolism

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline – Clara Barrios – PLOS ONE

Editorial: Microbiome reflects status of RA and response to therapy – Robert Phillips – Nature Reviews Rheumatology

Microbiome models

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus – Kristian Daly – Environmental Microbiology

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model – Eric M. Brown – Nature Communications

Animal microbiome

Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose – Masahiro Yuki – Environmental Microbiology

Two gut community enterotypes recur in diverse bumblebee species – Jilian Li- Current Biology

Unique metabolites protect earthworms against plant polyphenols – Manuel Liebeke – Nature Communications

Streptococcus panodentis sp. nov., from the oral cavities of chimpanzees – Masaaki Okamoto – Microbiology and Immunology

Plant, root, and soil microbiome

Fungal root endophytes of Quercus robur subjected to flooding – H. Kwaśna – Forest Pathology

Land Use and Precipitation Affect Organic and Microbial Carbon Stocks and the Specific Metabolic Quotient in Soils of Eleven Ecosystems of Mt. Kilimanjaro, Tanzania – Holger Pabst – Land Degradation & Development

The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA – Laura Lee Sims – Mycologia

Bacterial community structures as a diagnostic tool for watershed quality assessment – Luigimaria Borruso – Research in Microbiology

Water microbiome

Planktonic and sedimentary bacterial diversity of Lake Sayram in summer – Lei Fang – Microbiology Open

Waste and bioreactor microbiome

Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages – Vahid Razaviarani – Bioresource Technology

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Metagenomics and bioinformatics

Xander: employing a novel method for efficient gene-targeted metagenomic assembly – Qiong Wang – Microbiome

Metabolomics

Symposium report: Olfaction in the Kidney: ‘Smelling’ gut microbial metabolites – Niranjana Natarajan and Jennifer L. Pluznick – Experimental Physiology

Microbial Ecology

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment – Hasan Celiker & Jeff Gore – Nature Communications

Microbes in the news

Interview with Peter DiLaura, CEO of Second Genome: Data Mining The Microbiome Toward A Cure For Inflammatory Disease – Peter High – Forbes

Weight loss surgery benefits for gut microbiome last at least a decade – MedicalXpress

Extreme weight loss surgery works, but is it thanks to the knife—or the microbes? – Mitch Leslie – Science

A Belated Look at New York’s Cooling Towers, Prime Suspect in Legionnaires’ Outbreak – Winnie Hu and Noah Remnick – NY Times

Amid Legionnaires’ Fears, City Proposes New Cooling Tower Rules – Mara Gay and Corinne Ramey – Wall Street Journal
Randomised clinical study: Aspergillus niger-derived enzyme digests gluten in the stomach of healthy volunteers – B. N. Salden – Alimentary Pharmacology & Therapeutics

Study: Citrus Greening Bacterium Gives Vector Unexpected Boost – Paul Rusnak – Growing Produce

Team identifies mutations that allow bacteria to resist antibiotics – Phys.org

Africa is within reach of being declared a polio free region – The Conversation

Viruses Thrive In Big Families, In Sickness and In Health – University of Utah

Science, career, and publishing

Where Next for Genetics and Genomics? – Chris Tyler-Smith – PLOS Biology

Tech Women Triumph: $30k Funding In A Day, Success Under Pressure, True Leaders Inspire – Leo King – Forbes

#ilooklikeanengineer wants to challenge your ideas about who can be a scientist – Susan Svrluga – Washington Post

#FieldWorkFail: Gluing Yourself to a Live Crocodile and Other Mistakes: Scientists share the gross, scary, and often hilarious reality of doing experiments in the wild – Robinson Meyer – The Atlantic

9 Scientists Told Us What Scares Them The Most – Kelly Oakes – BuzzFeed

Bik’s Picks

Jack the Ripper’s final victim set to be exhumed following new theory on the killer’s identity – Doug Bolton – Independent

Scientists unearth earthworm’s ability to digest plant toxins – LiveMint

Are monarch butterflies really being massacred? A new study says it’s a lot more complicated than it seems – Sarah Kaplan – Washington Post

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August 4, 2015

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Diet-induced metabolic changes, rhythmicity of mouse gut microbiome, the microbiome of Lake Michigan, and chicken skin virome.

General microbiome

Antibiotics, microbiota and health: are there dangers hiding in plain sight? – A. Clinton White Jr – Current Opinion in Infectious Diseases

Short Course in the Microbiome: Meeting Dispatch – Kimberly Falana – Journal of Circulating Biomarkers

Pregnancy and birth microbiome

Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life – Corvaglia, Luigi – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome – Saeed Shoaie – Cell Metabolism

Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers – Juana I. Mosele – Molecular Nutrition & Food Research

Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults – Julien Tap – Environmental Microbiology

Review: The intestinal microbiome and health – Susan Tuddenham – Current Opinion in Infectious Diseases

Review: Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet – Cristiane Moraes – Journal of Renal Nutrition

Review: Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid – Cuong D Tran – Future Medicine

Microbiome models

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock – Xue Liang – PNAS

Viability of gut microbes as a complementary earthworm biomarker of metal exposure – Shin Woong Kim – Ecological Indicators

Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles – Troy D. Hubbard – Scientific Reports

Which games are growing bacterial populations playing? – Xiang-Yi Li – Interface

Animal microbiome

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin – Caroline Denesvre – Virus Genes

Variations in microbiota of culex (melanoconion) ocossa and culex (culex) declarator across periurban and rural environments – M Nelson Starkey – Honors Thesis – Andrews University

Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyzes the conversion of the plant toxin 2-phenylethyl isothiocyanate – Cornelia U. Welte – Environmental Microbiology

Plant, root, and soil microbiome

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
Shengjing Shi – mBio

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities – Michael S. Strickland – Frontiers in Microbiology

Changes in soil microbial community functionality and structure in a metal-polluted site: The effect of digestate and fly ash applications – M. Garcia-Sánchez – Journal of Environmental Management

Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species – Hieu X. Cao – Frontiers in Microbiology

Microbial composition alters the response of litter decomposition to environmental change – Kristin L. Matulich – Ecology

Plant community richness and microbial interactions structure bacterial communities in soil – Daniel C. Schlatter – Ecology

Plant diversity effects on soil microbial functions and enzymes are stronger than warming in a grassland experiment – Katja Steinauer – Ecology

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging – Chris Greening – PNAS

Review: Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review – L. Lagos – Journal of soil science and plant nutrition

Review: Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering – Liliana Quiza – Frontiers in Plant Science

Water microbiome

The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems – Clara Ruiz-González – Global Ecology and Biogeography

Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan – Suvendu Das – Microbial Ecology

Freshwater ice as habitat: Partitioning of phytoplankton- and bacteria between ice and water in central European reservoirs – R.M.L. McKay – Environmental Microbiology Reports

Urban microbial ecology of a freshwater estuary of Lake Michigan – Jenny C. Fisher – Elementa

Review: Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways – Thomas A. Bobik – Molecular Microbiology

Metagenomics and bioinformatics

SuRankCo: supervised ranking of contigs in de novo assemblies – Mathias Kuhring – BMC Bioinformatics

More microbe research

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri – Thomas R Conno – eLIFE

The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens” – Geng Zou – Scientific Reports

Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis – Tanmoy Roychowdhury – Scientific Reports

Protein synthesis by ribosomes with tethered subunits – Cédric Orelle – Nature

Long-term social dynamics drive loss of function in pathogenic bacteria – Sandra Breum Andersen – PNAS

New approaches to understanding the immune response to vaccination and infection –
David Furman – Vaccine

Microbes in the news

Would You Wear a Face Mask Made From Bacteria? – Jenna Rosenstein – Allure

Times-Picayune asks – Did a moldy building kill 4 New Orleans Professors – Jonathan Eisen – MicroBEnet

How the bugs in your gut keep you healthy – Keri Wiginton – Chicago Tribune

Scientists successfully breed symbiotic bacteria in mosquitoes to control dengue fever – ZeeNews India

Weight-Loss Surgery Changes Gut Bacteria – Rachael Rettner – Live Science

Volcanic bacteria take minimalist approach to survival – Otago University

Science, publishing, and career

Achieving Speaker Gender Equity at the American Society for Microbiology General Meeting – Arturo Casadevall – mBio

Bik’s Picks

This one was striking: Lightning strike as a possible cause of mortality of Australian sea lions, Neophoca cinerea – Peter D. Shaughnessy – Marine Mammal Science

Chilly at Work? Office Formula Was Devised for Men – Pam Belluck – New York Times
Belongs to: Energy consumption in buildings and female thermal demand – Boris Kingma & Wouter van Marken Lichtenbelt – Nature Climate Change

This Map Shows How New Yorkers View The Rest Of The United States. Finally, proof! – Carly Ledbetter – Huffington Post

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August 1, 2015

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So many new papers, so here is another Saturday installment of The Digest. Several papers on microbiome during pregnancy or the first months of life, ear infections, having older siblings, rhizosphere on volcanic islands, and aquatic fungal communities.

General human microbiome

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota – David J. Roach – PLOS Genetics

Opinion: The human–microbe metaorganism, evolution and extraterrestrial colonization – Leonard A Mermel – Future Microbiology

Frailty and the Microbiome – Meehan C.J. – Frailty in Aging

Pregnancy and birth microbiome

Secretor Status Is Strongly Associated with Microbial Alterations Observed during Pregnancy – Himanshu Kumar – PLOS ONE

Longitudinal Survey of Microbiota in Hospitalized Preterm Very Low Birth Weight Infants – Patel, Aloka L. – Journal of Pediatric Gastroenterology & Nutrition

Lactation and Intestinal Microbiota: How Early Diet Shapes the Infant Gut
Felicia Goldsmith – Journal of Mammary Gland Biology and Neoplasia

DGGE: Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Early Gut Colonization with Lactobacilli and Staphylococcus in Infants: the Hygiene Hypothesis Extended – Salminen, Seppo – Journal of Pediatric Gastroenterology & Nutrition

Association between positive urine cultures and necrotizing enterocolitis in a large cohort of hospitalized infants – Leslie C. Pineda – Early Human Development

Human oral microbiome

Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria – L. E. Chávez de Paz – International Endodontic Journal

Human respiratory microbiome

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation – Elise S. Cowley – mBio

Human skin and ear microbiome

The microbiome of otitis media with effusion in Indigenous Australian children – Jake Jervis-Bardy – International Journal of Pediatric Otorhinolaryngology

Review: Probiotics in personal care products – Mei-Chiung Jo Huang – Microbiology Discovery

Human gut microbiome

Having older siblings is associated with gut microbiota development during early childhood – Martin Frederik Laursen – BMC Microbiology

Serum Trimethylamine-N-Oxide is Elevated in CKD and Correlates with Coronary Atherosclerosis Burden – Jason R. Stubbs – Journal of the American Society of Nephrology

Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer – Zhiguang Gao – Molecular Medicine Reports

A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Review: Gut microorganisms as promising targets for the management of type 2 diabetes – Nathalie M. Delzenne – Diabetologia

Microbiome models

Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection – Andrew Leber – PLOS ONE

Evaluation of mucositis induced by irinotecan after microbial colonization in germ-free mice – Silvia H S P Pedroso – Microbiology

Animal microbiome

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow trout Oncorhynchus mykiss (Walbaum) using next generation sequencing (NGS) – Philip P. Lyons – Aquaculture Research

Plant, root, and soil microbiome

Rhizosphere on volcanic islands: Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands – Yoon-Jong Nam – The Journal of General and Applied Microbiology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Vulnerability of Soil and Its Associated Organic Matter to Degradation in a Subtropical Region: A Study From São Paulo State, Brazil – Alexandre Marco da Silva – Environment Quality Management

Effects of historical logging on soil microbial communities in a subtropical forest in southern China – Piao Song – Plant and Soil

Effects of rotifers, copepods and chironomid larvae on microbial communities in peatlands – Tomasz Mieczan – European Journal of Protistology

Methanogenic microbial community of the Eastern Paris Basin: Potential for energy production from organic-rich shales – Margaux Meslé – International Journal of Coal Geology

All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Phylogenetic structure of arbuscular mycorrhizal community shifts in response to increasing soil fertility – Yongjun Liu – Soil Biology and Biochemistry

Water and extremophile microbiome

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge – Erin M. Bertrand – PNAS

Effects of hydrostatic pressure on yeasts isolated from deep-sea hydrothermal vents – Gaëtan Burgaud- Research in Microbiology

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data – Katrin Panzer – PLOS ONE

Metaproteomics of aquatic microbial communities in a deep and stratified estuary – David Colatriano – Proteomics

Waste treatment microbiology

Review: Meta-omics approaches to understand and improve wastewater treatment systems – Elisa Rodríguez – Reviews in Environmental Science and Bio/Technology

Metagenomics and bioinformatics

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples – Tal Korem – Science

Spaced seeds improve k-mer-based metagenomic classification – Karel Břinda – Bioinformatics

Microbial Ecology

Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities – Cyrus A. Mallon – Ecology

Not sure if I like this term: Tritagonist as a new term for uncharacterised microorganisms in environmental systems – Florian M Freimoser – ISME Journal

Microbes in the news

Bacteria on chicken, turkey, pork linked to bladder infections – Lynne Terry – Oregon Live

Byproduct of intestinal bacteria may jeopardize heart health in kidney disease patients – Medical Xpress

Oregon architecture researchers to study indoor air quality in 72 homes – EurekAlert

Research spotlights a previously unknown microbial ‘drama’ playing in the Southern Ocean – Science Daily

Government of Canada Invests in New Western Canadian Microbiome Centre – Sys-Con Media

A Video of the destruction can be seen here: Wood-Decay Fungus Identified as Culprit Consuming Pomona Family’s Home – LA Testing

Microbes and Art

Don’t Be Grossed Out, The Bacteria On These Petri Dish Plates Is Art – Andrew Liszewski – Gizmodo

Call for Entries! ASM’s 2015 Agar Art Contest: Submit your work by September 3th – MicrobeWorld

Bik’s Picks: drought edition

Puget Sound sweltering from the drought and Blob – Department of Ecology – Courier Herald

Extreme Droughts Weaken Trees’ Ability to Soak Up Carbon – William R L Anderegg – Gizmodo

It’s Raining Spiders! Weirdest Effects of California Drought – Tia Ghose – Live Science

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July 31, 2015

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Microbiome antibodies prevented an HIV vaccine from working, effect of antibiotics during rhinosinusitis, microbiome and tuberculosis, how mussels get colonized, and a fruit based nutrient bar’s effect on human metabolism.

Human respiratory microbiome

The Microbiome at the Pulmonary Alveolar Niche: How It Affects the Human Innate Response against Mycobacterium tuberculosis – Alexander J. Adami – Tuberculosis

The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis – Mark A. Merkley – International Forum of Allergy & Rhinology

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Human gut microbiome

Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies – Wilton B. Williams – Science

Not microbiota, but of interest: Go with the Flow: Regional gastrointestinal transit and pH studied in 215 healthy volunteers using the wireless motility capsule: influence of age, gender, study country and testing protocol – Y. T. Wang – Alimentary Pharmacology & Therapeutics

Commentary: You Lose Some, You Win Some: Weight Loss Induces Microbiota and Metabolite Shifts – Elisabeth M. Bik – EBioMedicine

Review: The role of the gut microbiota in metabolic health – Aafke W. F. Janssen and Sander Kersten – The FASEB Journal

Microbiome models

MyD88 Adaptor-Dependent Microbial Sensing by Regulatory T Cells Promotes Mucosal Tolerance and Enforces Commensalism – Sen Wang – Immunity

Commentary: A Toolbox for Microbiome Engineering – Mohamed S. Donia – Cell Systems

Animal microbiome

The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease – Devin B. Holman – Veterinary Microbiology

Adapted to change: the rapid development of symbiosis in newly settled, fast-maturing chemosymbiotic mussels in the deep sea – Laming Sven R – Marine Environmental Research

Plant, soil, and root microbiology

Roots from distinct plant developmental stages are capable of rapidly selecting their own microbiome without the influence of environmental and soil edaphic factors – Jun Yuan – Soil Biology and Biochemistry

Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth – Sarah K. Hargreaves – PLOS ONE

Interactions between a plant growth-promoting rhizobacterium and smoke-derived compounds and their effect on okra growth – Heino B. Papenfus – Journal of Plant Nutrition and Soil Science

Food microbiology

Diversity and dynamics of antibiotic-resistant bacteria in cheese as determined by PCR denaturing gradient gel electrophoresis – Ana Belén Flórez – International Journal of Food Microbiology

Proteomics and metabolomics

A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation – Alessandro Tanca – Data in Brief

A multicomponent nutrient bar promotes weight loss and improves dyslipidemia and insulin resistance in the overweight/obese: chronic inflammation blunts these improvements – Joyce C. McCann – The FASEB Journal

Microbes in the news

Gut microbiome may have interfered with experimental HIV vaccines – Rachel Tompa – Fred Hutch

Vacation souvenirs can be crappy, but rarely are they actual crap: Ilana Brito, the Biologist Who Flew to Fiji for Feces – Rachel Becker – Ozy

Science, publishing, and career

Why not have a life? I only stay late if I’m actually doing an experiment – Gary McDowell – Science

Bik’s Picks

Deadly Fungus Could Threaten U.S. Salamanders – Stephanie Pappas – Discover / LiveScience

Plants send out stress signals just like animals, scientists find – Robert Gebelhoff – Washington Post

Vaccine Success Holds Hope For End To Deadly Scourge Of Ebola – Kate Kelland – Huffington Post

The world’s best whiskey is being sent into space for the sake of science – Gabriel Fisher – Quartz

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July 30, 2015

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Correct vocabulary of microbiome research, microbiome during mosquito development, microbes on Granada’s Royal Chapel stone, and microbes in Atacama desert.

General microbiome

About the proper use of “16S”, “microbiome”, and “microbiota”, and why “microflora” is not correct. Note Elies: But “microbiota” is a plant too!
The vocabulary of microbiome research: a proposal – Julian R. Marchesi – Microbiome

Human oral microbiome

Host response mechanisms in periodontal diseases – Nora Silva – Journal of Applied Oral Science

Human respiratory microbiome

The airway microbiome in patients with severe asthma: Associations with disease features and severity – Yvonne J. Huang – The Journal of Allergy and Clinical Immunology

Human gastric microbiome

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome – DeAnna E. Beasley – PLOS ONE

Microbiome models

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets – Nirupama Benis – BMC Genomics

Animal microbiome

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Review: The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals – A. Rodrigues Hoffmann – Veterinary Pathology

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi affect plant community structure under various nutrient conditions and stabilize the community productivity – Gaowen Yang – Oikos

Complementarity in both plant and mycorrhizal fungal communities are not necessarily increased by diversity in the other – Cameron Wagg – Journal of Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing –
Youwei Hong – Canadian Journal of Microbiology

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil – Abdullah M. Al-Sadi – BMC Microbiology

Mineralogy: Geochemical evidence of microbial activity within ooids – Mara R. Diaz – Sedimentology

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments – Isabel C. Romero – Journal of Marine Science and Engineering

Inexplicable Arsenic: Human Dimensions of Soil, Water, Food and Microbial
Resources – Ramakrishnan B – Journal of Environmetnal and Analytical Toxicology

Water microbiome

Structure of the archaeal community in the Black Sea photic zone – A. Y. Merkel – Microbiology

Review: Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes – Thomas Mock – Global Change Microbiology

Extremophiles

Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert – Maria Cecilia Rasuk – Microbial Ecology

Thesis: Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields – Matheus Carnevali, Paula B – University of Nevada, Reno

Waste and built environment microbiology

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters – Samik Bagchi – PLOS ONE

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada – Fadwa Jroundi – PLOS ONE

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil – Juliana Alves Resende – Microbial Ecology

Metagenomics and bioinformatics

deFUME: Dynamic exploration of functional metagenomic sequencing data – Eric van der Helm – BMC Research Notes

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Microbes in the news

Kingdoms are so 20th century: The tree of life gets a makeover: Schoolroom kingdoms are taking a backseat to life’s supergroups – Susan Milius – Science News

Soil-Dwelling Fungus Rode Joplin Tornado to Unexpected Human Home – Jennifer Frazer – Scientific American

Agave extracts show ability to shift gut microbiota: Ingredion study – Stephen DANIELLS – Nutraingredients

Bacterial Find Sheds Light on Digestive Issues, Diabetes, Obesity – American Crystallographic Association

Water At Some Olympic Venues In Rio de Janeiro Reportedly Contain Virus Levels On Par With Raw Sewage – Brad Brooks and Jeny Barchfield – Huffington Post

LASA students developing bacteria to improve carbon monoxide detectors – Calily Bien – KXAN

Bik’s Picks

A tragic death leaves just four northern white rhinos living and little hope for the species – Rachel Feltman – Washington Post

‘Once in a Blue Moon’ Happens on Friday — Why? – Geoff Gaherty – Discovery

How did you get that job: designing a parachute for NASA’s Mars rover – Elizabeth Lopatto – The Verge

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July 29, 2015

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Pack hunting by soil amoeba, microbiota of meconium and uterus, transcriptomics of oral phages, no differences in antibiotic resistance gene content in organic or regular pigs, and effects of IBD associated microbes on mouse physiology.

General microbiome

Editorial: News Feature: Microbes on the mind – Helen H. Shen – PNAS

Microbiome of pregnancy and birth

Note: just one sample was PCR positive: First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota – Richard Hansen – PLOS ONE

Understanding the Biologic Therapies of Probiotics, Prebiotics, and Synbiotics: Exploring Current Evidence for Use in Premature Infants for the Prevention of Necrotizing Enterocolitis – Asmerom, Mussie – Journal of Perinatal & Neonatal Nursing

Human oral microbiome

Transcriptome analysis of bacteriophage communities in periodontal health and disease – Tasha M. Santiago-Rodriguez – BMC Genomics

Human respiratory microbiome

Paired analysis of the microbiota of surface mucus and whole-tissue specimens in patients with chronic rhinosinusitis – Raymond J.T. Kim – International Forum of Allergy & Rhinology

Human genital microbiome

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene – Hans Verstaelen – PeerJ

Human skin microbiome

Review: Regulation of T cell immunity in atopic dermatitis by microbes: the Yin and Yang of cutaneous inflammation – Tilo Biedermann – Frontiers in Immunology

Human gut microbiome

Ruminococcal cellulosomes: molecular Lego to deconstruct microcrystalline cellulose in human gut – Gurvan Michel – Environmental Microbiology

Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons – Jelena Vulevic – British Journal of Nutrition

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Editorial: Gut microbiota: Microbiota and neuroimmune signalling—Metchnikoff to microglia – John F. Cryan & Timothy G. Dinan

Review: A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Editorial: Stool microbiome changes in VEGF-TKI-induced diarrhoea – Nature Reviews Urology

Models of microbiome research

Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice – Thomas W Hoffmann – ISME Journal

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention – Rita-Marie McFadden – Inflammatory Bowel Diseases

Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia –
Stefanie Gauguet – Infection and Immunity

Oral Administration of P. gingivalis Induces Dysbiosis of Gut Microbiota and Impaired Barrier Function Leading to Dissemination of Enterobacteria to the Liver – Mayuka Nakajima – PLOS ONE

Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis – Ming Li – Frontiers in Microbiology

Symbiotic maple saps minimize disruption of the mice intestinal microbiota after oral antibiotic administration – Riadh Hammami – International Journal of Food Sciences and Nutrition

Animal microbiome

Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries – Lenka Gerzova – PLOS ONE

Symbiotic bacteria enable olive fly larvae to overcome host defences – Michael Ben-Yosef – Royal Society Open Science

Plant, root, and soil microbiome

Not sure where to file this one under, but pretty cool: Pack hunting by a common soil amoeba on nematodes – Stefan Geisen – Environmental Microbiology

Anaerobic degradation pathway of the novel chiral insecticide Paichongding and its impact on bacterial communities in soils – Zhiqiang Cai – Journal of Agricultural and Food Chemistry

Metagenomics and bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metabolomics and Proteomics

Effects of Dietary Different Doses of Copper and High Fructose Feeding on Rat Fecal Metabolome – Xiaoli Wei – Journal of Proteome Research

Science, publishing, and career

Let’s Make Gender Diversity in Data Science a Priority Right from the Start – Francine D. Berman – PLOS Biology

Microbes in the news

What are ‘eye crusties’ made of? uBiome asking for participants to use their eye kit

Bacteria Hysteria

Germaphobes look away! Your gym bag might contain high levels of bacteria usually found in faeces – Irish Examiner

Bik’s Picks

A Skeleton, a Catholic Relic, and a Mystery About American Origins – Adrienne Lafrance – The Atlantic

The confounding case of the missing carbon – Michael Casey – CBS News

Washington Is Finally Getting What It Deserves As It Sinks Into The Sea – Kate Sheppard – Huffington Post

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July 28, 2015

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A review of the human hand microbiome, microbiome and anxiety in mouse models, diabetes, bacteria in thrombolites, how plants recruits microbial symbionts, towards a standard in microbial genome annotation, and an article about the lab of Jill Banfield.

Microbiome of pregnancy and birth

Prevalence of oral Candida in the first year of life – C. Stecksén-Blicks – Mycoses

Cross-colonization of infants with probiotic organisms in a neonatal unit – L. Hickey – Journal of Hospital Infection

Human oral microbiome

Periodontal microbiota and phospholipases: The Oral Infections and Vascular Disease Epidemiology Study (INVEST) – Adrien Boillot – Atherosclerosis

Review: Alterations of the oral microbiota and oral clinical findings in dry mouth – Y. Hayashi – Journal of Oral Biosciences

Human skin and eye microbiome

Review of Human Hand Microbiome Research – Sarah L. Edmonds-Wilson – Journal of Dermatological Research

Correspondence: Harnessing the microbiome in glaucoma and uveitis – Ankur Gupta – Medical Hypotheses

Human respiratory microbiome

High diversity of non-sporulating moulds in respiratory specimens of immunocompromised patients: should all the species be reported when diagnosing invasive aspergillosis? – Dea Garcia-Hermoso – Mycoses

 

Human gut microbiome

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment – Xuan Zhang – Nature Medicine

A tough pill to swallow (perspective): Ready for Oral Fecal Microbiota Pill in Clinical Practice? – Timothy Nguyen – The Journal for Nurse Practitioners

Review: The human gut microbiota and virome: potential therapeutic implications – Emidio Scarpellini – Digestive and Liver Disease

Review: Intestinal Immunity and Gut Microbiota as Therapeutic Targets for Preventing Atherosclerotic Cardiovascular Diseases – Tomoya Yamashita – Circulation Journal

Microbiome models

Microbiota and host determinants of behavioural phenotype in maternally separated mice – G. De Palma – Nature Communications

Microbiota regulates type 1 diabetes – Michael P Burrows – PNAS

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon – Noortje Ijssennagger – PNAS

Intestinal inhibition of Atg7 prevents tumour initiation through a microbiome-influenced immune response and suppresses tumour growth – Jonathan Lévy – Nature Cell Biology

Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing – Jong Pyo Chae – Animal Feed Science and Technology

Dynamic Metabonomic and Microbiological Response of Rats to Lincomycin Exposure: An Integrated Microbiology and Metabonomics Analysis – Manna Lin – RSC Advances

Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet – Aline Rissetti Roquetto – Food Research International

Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection – Hyeon-Woo Koh – Microbes and Environments

Review: Interrelatedness Between Dysbiosis in the Gut Microbiota Due to Immunodeficiency and Disease Penetrance of Colitis – Avijit Ray – Immunology

Animal microbiome

Experimental studies of microbial populations and incidence of zoonotic pathogens in the faeces of red deer (Cervus elaphus) – Sebastian Gnat – Letters in Applied Microbiology

Yeast microbiota of natural cavities of manatees (Trichechus inunguis and T. manatus) in Brazil and its relevance for animal health and management in captivity – José J.C. Sidrim – Canadian Journal of Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata – Sara Cortés-Lara – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling – J. M. Mobberley – Scientific Reports

Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden – Hanna Millberg – Fungal Ecology

Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant – Nicola J. Day – Journal of Ecology

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK) – Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Alder trees enhance crop productivity and soil microbial biomass in tea plantations – P.E. Mortimer – Applied Soil Ecology

Perspective: Plant genotype, microbial recruitment and nutritional security – Jai S. Patel – Frontiers in Plant Science

I don’t always have symbionts, but when I do, I prefer alphaproteobacteria: Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts – Cyril Bontemps – New Phytologist

Conference abstract: Changes in rhizosphere microbiome from halotolerant tomato are correlated with physiological and biochemical parameters of oxidative stress in plants – Radu Liviu Sumalan – Journal of Biotechnology

Review: Root associated bacteria – Friends or enemies? A review – Gabriela Mihalache – Memoirs of the Scientific Sections of the Romanian Academy

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories? – A. Blaud – Biology and Fertility of Soils

Water microbiome

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties – Bei-bei Chai – Journal of Environmental Biology

Extremophiles

Review: Microbial communities and primary succession in high altitude mountain environments – Sonia Ciccazzo – Annals of Microbiology

Metagenomics and bioinformatics

FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing – Rahul Sharma – Mycological Progress

Toward a standard in structural genome annotation for prokaryotes – H. James Tripp – Standards in Genomic Sciences

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria – Cindy Shi – SciTech Connect

Microbial Ecology

Socially mediated induction and suppression of antibiosis during bacterial coexistence
Monica I. Abrudan – PNAS

Microbes in the news

About work in the lab of Jill Banfield: At Tiny Scales, a Giant Burst on Tree of Life – Kevin Hartnett – Quanta Magazine

Swan song for antibiotics? Can phage therapy and gene editing fill the gap? – Nicholas Staropoli – Genetic Literacy Project

Metagenomic Study Finds Differences in Oral, Gut Microbiomes of Rheumatoid Arthritis Patients – Genome Web

Your Burger Is Full of Living Things, Even If It’s Vegetarian – Maddie Stone – Gizmodo

Title incorrect, it’s a Yersinia, but different species: A Species Of Bacteria That Causes Bubonic Plague And Other Disease In Salmon May Also Be Able To Treat Cancer – Lecia Bushak – Medical Daily

Bacteria in gut profiling secret to healthy weight – Peta Bee – The Australian

Bacteria to protect Appenzeller cheese from fakes – Anand Chandrasekhar – SwissInfo

Grandparents largely to blame for China’s spiking childhood obesity, Microbiota treatment sees dramatic results in obese children – RJ Whitehead – FoodNavigator

Bik’s Picks

Reception of odors and repellents in mosquitoes – Anandasankar Ray – Current Opinion in Neurobiology

570 Sea Turtle Hatchlings Are Released Into Atlantic Ocean – Getty Images

Everything you need to know about lactose intolerance – with maps! – New Scientist

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