September 29, 2017

Today’s digest is a delight for dog lovers – an interesting look at the nasal microbiome of dogs and two interesting studies on freshwater phages. Lastly, researchers in South Korea establish a human stool bank.

Human Gut Microbiome

REVIEW: A review of the relationship between the gut microbiota and amino acid metabolism

Lin R.Amino Acids

Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

Yacoub R. PloS one

Oral Microbiome

Exploring the salivary microbiome of children stratified by the oral hygiene index

Mashima I. PLoS ONE

Animal experiments and microbiome

Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs Part 2: Ewe lamb rumen microbial communities

Ishaq SL. Journal of Animal Science

Characterization of the nasal and oral microbiota of detection dogs

Isaiah A. PLoS one

Marine and Inland Water microbiome

Biodiversity and species competition regulate the resilience of microbial biofilm community

Feng K. Molecular Ecology

Plant and soil microbiome

The Fructan Syndrome: Evolutionary Aspects and Common Themes Among Plants and Microbes

Versluys M. Plant, Cell & Environment

Agricultural land use determines functional genetic diversity of soil microbial communities

Manoharan L. Soil Biology and Biochemistry

Synergetic suppression of soybean cyst nematodes by chitosan and Hirsutella minnesotensis via the assembly of the soybean rhizosphere microbial communities

Mwaheb MAMA .Biological Control

Patterns and mechanisms of responses by soil microbial communities to nitrogen addition

Zhou Z. Soil Biology and Biochemistry

Links between plant and fungal diversity in habitat fragments of coastal shrubland.

Maltz MR. PloS one

The response of soil bacterial communities to mining subsidence in the west China aeolian sand area

Shi P. Applied Soil Ecology

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

Moussa TAA. PLoS one

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

David AS. Molecular Ecology

Virome

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the deep chlorophyll maximum of the South China Sea

Xie ZX. Environmental Microbiology

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Moon K. Environmental Microbiology

Protocol

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA …

Han P. Applied Microbiology and Biotechnology

Use of RNALater® Preservation for Virome Sequencing in Outbreak settings

Kohl C.Frontiers in Microbiology

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince C. Genome Biology

Microbiome News

Korea’s first stool bank gets down to business

-Korean Biomedical Review

September 24, 2017

Posted on September 24, 2017 by Kiran

Events and jobs

Microbiology Non Registered Technician – Seattle, Washington – Work Schedule: Sunday – Thursday, 11:00pm – 7:30am

General microbiome

The Gram-positive model organism Bacillus subtilis does not form detectable cardiolipin-specific lipid domains – AR Pogmore – bioRxiv

Multi-site human microbiome

USA300 MRSA lineages persist on multiple body sites following infection – TD Read – bioRxiv

Human oral microbiome

Review: The role of wine and food polyphenols in oral health – A Esteban-Fernández – Trends in Food Science & Technology

Human skin microbiome

The micro-evolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare – CP Harkins – Journal of Investigative Dermatology

Human gut microbiome

Chapter: Bifidobacteria: Ecology and Coevolution With the Host – F Turroni – The Bifidobacteria and Related Organisms

Stress Responses of Bifidobacteria: Oxygen and Bile Acid as the Stressors – S Kawasaki – The Bifidobacteria and Related Organisms

Gut microbiota and the liver. – A Federico – Minerva Gastroenterologica e Dietologica.

Animal microbiome

Chapter: Honeybee-Specific Bifidobacteria and Lactobacilli – T Olofsson – The Bifidobacteria and Related Organisms

Antimicrobial resistant Escherichia coli in the reproductive tract microbiota of cows and sows – AT Luque – Comparative Immunology, Microbiology and Infectious Diseases

Review: Mechanisms of Plasmodium-Enhanced Attraction of Mosquito Vectors – AO Busula – Trends in Parasitology

Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts – BER Rubin – bioRxiv

Plant, root, and soil microbiome

Conservation tillage enhances the stability of the rhizosphere bacterial community responding to plant growth – Z Wang – Agronomy for Sustainable Development

Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion – MA Anthony – Ecosphere

Effects of exogenously applied salicylic acid and putrescine alone and in combination with rhizobacteria on the phytoremediation of heavy metals and chickpea growth in sandy soil. – N Khan – International Journal of Phytoremediation

Built environment

Medium shapes the microbial community of water filters with implications for effluent quality – M Vignola – Water Research

Food microbiology

Effects of the predominant bacteria from meju and doenjang on the production of volatile compounds during soybean fermentation – DW Jeong – International Journal of Food Microbiology

Predominant yeasts in Chinese traditional sourdough and their influence on aroma formation in Chinese steamed bread – T Liu – Food Chemistry

Chapter: Microbial Pigments From Bacteria, Yeasts, Fungi, and Microalgae for the Food and Feed Industries – L Dufossé – Food Dyes

Phages and viruses

An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach. – K Parmar – Current Microbiology

Techniques

Isolation, Cultivation, and Storage of Bifidobacteria – M Modesto – The Bifidobacteria and Related Organisms

Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics – M Price – bioRxiv

Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method. – A Dilhari – AMB Express

Fecal microbiota transplantation: past, present and future perspectives. – S Bibbò – Minerva Gastroenterologica e Dietologica.

Microbes in the news

I Sent Away a Sample of My Poop, and Here’s What I Learned About My Health – Pop Sugar

DESPERATE ACT Mum-of-one who’s spent £37k on surgery now injects herself with BACTERIA in an attempt to look younger – The Sun

What’s Next for Assembly Biosciences Incorporated (NASDAQ:ASMB) After Having Less Shares Shorted? – The Press Telegraph

Your Towels Are Way Dirtier Than You Think – Time

Cnidarians remotely control bacteria – Phys.org

Mysterious flesh-eating bacteria is raging in Australia – ARS Technica

Lipid vesicles replace blood in new bacteria test – Phys.org

DEATH BY HURRICANE: THERE COULD SOON BE A CURE FOR A FLESH-EATING BACTERIA THAT ALMOST JUST KILLED A MAN IN TEXAS – News Week

Swiss startup says high-tech water filter can remove bacteria, viruses and plastic – Market Watch

Buruli ulcer: How to avoid being infected by gruesome flesh-eating bacteria – Abc.net

September 21, 2017

Posted on September 21, 2017 by anjacobson

Additional data and new analyses from the NIH Human Microbiome Project, understanding lambda phage integration in its effects on the host, a yeast fermentation method for use in wine making.

Pregnancy and early life

Pre-print: Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing – Anuradha Ravi – bioRxiv

Multi-site human microbiome

Strains, functions and dynamics in the expanded Human Microbiome Project – Jason Lloyd-Price – Nature

Phages and viruses

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology – Yu Tanouchi – mBio

Techniques

The 16S rRNA gene-based PCR method used for the detection of segmented filamentous bacteria in the intestinal microbiota generates false-positive results – Forough L Nowrouzian – Acta Pathologica, Microbiologica, et Immunologica Scandinavica

Pre-print: Wine yeast phenomics: a standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions – Emilien Peltier – bioRxiv

More microbes

Pre-print: Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – Corey S Westfall – bioRxiv

Microbes in the news

What’s the latest on gut microbiota? Concordia microbiology undergrads publish their findings – Phys.Org

Microbes on the market

Ixcela Launches Over-the-Counter Gut Health Test and Sophisticated Internal Wellness Program – Business Wire

Avadim Technologies Inc. Announces Partnership With Cardinal Health, Inc. – Market Wired

September 20, 2017

Posted on September 20, 2017 by Kiran

General microbiome

The human bitter taste receptor T2R38 is broadly tuned for bacterial compounds – C Verbeurgt – PLoS One

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities. – J Juhász – Biology Direct

Applying allometric theory to fungi – CA Aguilar-Trigueros – The ISME Journal

The Editorial on the Research Topic The Impact of Microorganisms on Consumption of Atmospheric Trace Gases – S Kolb – Frontiers in Microbiology

Human oral microbiome

Variations in oral microbiota associated with oral cancer. – H Zhao – Scientific Reports

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. – M Kuboniwa – Nature Microbiology

Human gut microbiome

Normalization of the microbiota in patients after treatment for colonic lesions – MA Sze – bioRxiv

Review: Modulation of the gut microbiome: a systematic review of the effect of bariatric surgery. – Y Guo – European Journal of Endocrinology

Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. – T Pavlova – Analytica Chimica Acta

Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. – K Winglee – Microbiome

Continued Alcohol Misuse in Human Cirrhosis is Associated with An Impaired Gut-Liver Axis. – JS Bajaj – Alcoholism, Clinical and Experimental Research

Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population. – F Liu – Scientific Reports

Animal experiments

Experimental colitis delays and reduces the severity of collagen-induced arthritis in mice – J Hablot – PLoS One

Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA – M DiMarzio – PLoS One

The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice – M Elderman – PLoS One

Review:Role of the gastrointestinal microbiota in small animal health and disease. – A Redfern – The Veterinary Record

Gut Microbiota and IL-17A: Physiological and Pathological Responses. – B Douzandeh-Mobarrez – Probiotics and Antimicrobial Proteins

Animal microbiome

The microbiota of water buffalo milk during mastitis – C Catozzi – PLoS One

What determines sclerobiont colonization on marine mollusk shells? – VO Agostini – PLoS One

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. – KH Sharp – Microbiome

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen. – HT Do – Asian-Australasian Journal of Animal Sciences

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India. – SS Charan – Medical and Veterinary Entomology

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. – F Cornejo-Granados – Scientific Reports

Plant, root, and soil microbiome

Evolution with a seed bank: the population genetic consequences of microbial dormancy – WR Shoemaker – bioRxiv

Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longispora albida and Longisporafulva. – C Piao – International Journal of Systematic and Evolutionary Microbiology

Actinomycetes benefaction role in soil and plant health. – AA Bhatti – Microbial Pathogenesis

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation – I Alkorta – FEMS Microbiology Letters

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. – L Zhang – FEMS Microbiology Ecology

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. – M Delgado-Baquerizo – Ecology Letters

Paenibacillus arcticus sp. nov., isolated from Arctic soil. – IT Cha – International Journal of Systematic and Evolutionary Microbiology

Mineral phosphorus fertilization modulates interactions between maize, rhizosphere yeasts and arbuscular mycorrhizal fungi – M Sarabia – Rhizosphere

Zinc Solubilizing Bacillus cereus and related species Modulates Growth, Yield and Zinc Biofortification of Soybean and Wheat Seeds Cultivated in Central India – R Khande – Rhizosphere

Utilisation of mucilage C by microbial communities under drought – MA Ahmed – Biology and Fertility of Soils

Built environment

Walker occupancy has an impact on changing airborne bacterial communities in an underground pedestrian space, as small-dust particles increased with raising both temperature and humidity – T Okubo – PLoS One

Food microbiology

Diversity and dynamics stability of bacterial community in traditional solid-state fermentation of Qishan vinegar – X Gan – Annals of Microbiology

Phages and viruses

Isolation and identification of enteroviruses from sewage and sewage-contaminated water samples from Ibadan, Nigeria, 2012-2013. – JA Adeniji – bioRxiv

The virome of Drosophila suzukii, an invasive pest of soft fruit – NC Medd – bioRxiv

Immune Loss as a Driver of Coexistence During Host-Phage Coevolution – JL Weissman – bioRxiv

Bioinformatics

Bioinformatics in the Netherlands: the value of a nationwide community – CWG van Gelder – Briefings in Bioinformatics

Techniques

Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires – B Lia – PLoS One

Methods matter: Influential purification and analysis parameters for intracellular parasite metabolomics – MA Carey – bioRxiv

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome – RR Rodrigues – bioRxiv

Quorum sensing improves current output with Acidithiobacillus ferrooxidans. – N Chabert – Microbial Biotechnology

Transcriptome analysis of Pseudostellaria heterophylla in response to the infection of pathogenic Fusarium oxysporum. – X Qin – BMC Plant Biology

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. – Y Daquerre – BMC Genomics

Microbes in the news

Rocks, not bacteria, triggered Earth’s oxidation – Cosmos

The Table At Your Favorite Restaurant May Be Way Grosser Than You Thought The Table At Your Favorite Restaurant May Be Way Grosser Than You Thought – Men’s Health

Researchers unlock potential pathway to treat flesh-eating bacteria – Phys.org

Revealed: The nasty infections you can pick up at the gym – and how to avoid deadly bacteria lingering on your workout gear – Daily Mail Online

Flagship seeks $500M for sixth fund; unveils another microbiome firm – Fierce Biotech

CAN SPRAYING BACTERIA IN YOUR FACE ACTUALLY HAVE HEALTH BENEFITS? – CDA Press

Space-Grown Bacteria Could Pose Major Problems for Astronauts – Health Line

See jerkface bacteria hiding in tumors and gobbling chemotherapy drugs – Ars Technica

How BIOHM’s At Home Candida Test Is Giving Consumers Peace of Mind – Forbes

September 16, 2017

Posted on September 16, 2017 by Kiran

Events and jobs

Interim Microbiology Manager – Central Belt – North Lanarkshire, Scotland, UK

General microbiome

Haloarchaea: worth exploring for their biotechnological potential – A Singh – Biotechnology Letters

Pregnancy and early life

Rotavirus Vaccine Response Correlates with the Infant Gut Microbiota Composition in Pakistan – V Harris – Gut Microbes

Human gut microbiome

Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition – TP Jenkins – PLoS One

Animal experiments

Review: Gut Microbial Influences on the Mammalian Intestinal Stem Cell Niche. – BCE Peck – Stem Cells International

Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota – C Fraumene – Gut Microbes

SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract – KB Uldahl – Journal of Applied Microbiology

Fungal derived 15-keto-prostaglandin E₂ activates host peroxisome proliferator-activated receptor gamma (PPAR-γ) to promote C. neoformans growth during infection. – RJ Evans – bioRxiv

The effect of regular or reduced-fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community – E Castillo-Lopez – Journal of Applied Microbiology

Role of Microbiota in Strengthening Ocular Mucosal Barrier Function Through Secretory IgA – A Kugadas – IOVS

Animal microbiome

Virome analysis for identification of novel mammalian viruses in bats from Southeast China. – D Hu – Scientific Reports

Plant, root, and soil microbiome

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems – D Sharma-Poudyal – PLoS One

Nitrile-Degrading Bacteria Isolated from Compost – R Egelkamp – Frontiers in Environmental Science

Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria – BS Mickan – Biology and Fertility of Soils

High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits – P Nutaratat – 3 Biotech

Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii – J Luo – Applied Microbiology and Biotechnology

Water microbiome and extremophile

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – A Pontefract – Frontiers in Microbiology

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia) – A Brouchkov – Gene

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage – V Mesa – Frontiers in Microbiology

Techniques

Review: Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics – E Stylianou – Molecular Diagnosis & Therapy

Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA – E Erskine – bioRxiv

IN VITRO AND IN VIVO CHARACTERISATION OF ISOLATES OF CRYPTOCOCCUS NEOFORMANS CAUSING MENINGITIS IN HIV-INFECTED AND UNINFECTED PATIENTS IN VIETNAM – TT Lam – bioRxiv

Morphological and Transcriptomic analysis reveals the osmoadaptive response of endophytic fungus Aspergillus montevidensis ZYD4 to high salt stress – KH Liu – Frontiers in Microbiology

Multilocus and SSU rRNA gene phylogenetic analyses of available cyanobacterial genomes, and their relation to the current taxonomic system – J Mareš – Hydrobiologia

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing – X Li – Frontiers in Microbiology

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition – JA Lee – Environmental Microbiology

Microbes in the news

WITH DESIGNER BACTERIA, CROPS COULD ONE DAY FERTILIZE THEMSELVES – Wired

Omega 3 intake linked to greater gut microbial diversity – Nutra Ingredients

Scientists Just Discovered Organisms That Are Distinct From Any Life Forms Known to Science – Futurism

September 15, 2017

Posted on September 15, 2017 by TinaS

Events and jobs

Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

General microbiome

Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou – Critical Reviews in Food Science and Nutrition

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

Pregnancy and early life

The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

Human respiratory microbiome

Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

Human nearly-sterile sites

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

Human gut microbiome

Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck – mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

Animal experiments

Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

Animal microbiome

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu – Proceedings of the Royal Society of London B

Plant, root, and soil microbiome

Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia – Keith Christian – Ecology & Evolution

Food microbiology

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

Microbes in the news
NIPGR scientists identify bacteria that can devour fungi

Are Genes to Blame for Cavity-causing Bacteria?

Microbes on the market (news about biotech companies)

Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

Inventor converts waste plastics to fertilizer, fuel

Science, publishing, and career

The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine

September 9, 2017

Posted on September 9, 2017 by Kiran

Pregnancy and early life

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants – MA Stanislawski – Microbiome

Human oral microbiome

The tongue microbiome in healthy subjects and patients with intra-oral halitosis – SK Seerangaiyan – Journal of Breath Research

Effects of lactoferrin and lactoperoxidase-containing food on the oral microbiota in the elderly – M Nakano – Microbiology & Immunology

Unraveling the human salivary microbiome diversity in Indian populations – A Sarkar – PLoS One

Human gut microbiome

Review: Influence of gut microbiota on the development and progression of nonalcoholic steatohepatitis – F de Faria Ghetti – European Journal of Nutrition

Markers of intestinal permeability are already altered in early stages of non-alcoholic fatty liver disease: Studies in children – A Nier – PLoS One

Review: the human intestinal virome in health and disease – SR Carding – AP &T

Meds Modify Microbiome, Mediating Their Effects – NM Koropatkin – Cell Metabolism

Animal experiments

Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring – JC Needell – PLoS One

The intestinal microbiota determines the colitis-inducing potential of T-bet-deficient Th cells in mice – J Zimmermann – European Journal of Immunology

A study of the prebiotic-like effects of tomato juice consumption in rats with diet-induced non-alcoholic fatty liver disease (NAFLD). – FJ García-Alonso – Food & Function

Patterns of host gene expression associated with harboring a foregut microbial community. – KD Kohl – BMC Genomics

Animal microbiome

Bacterial community composition and distribution in different segments of the gastrointestinal tract of wild-caught adult Penaeus monodon – P Mongkol – Aquaculture Research

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – V Lemieux-Labonté – Microbiome

Plant, root, and soil microbiome

Soil microbiomes associated with Verticillium wilt suppressive broccoli and chitin amendments are enriched with potential biocontrol agents. – P Inderbitzin – Phytopathology

Olive mill waste and glyphosate-based herbicide addition to olive grove soils: effects on microbial activities and their responses to drying–rewetting cycles – N Boukhdoud – Soil Use and Management

Changes in soil microbial communities after 10 years of winter wheat cultivation versus fallow in an organic-poor soil in the Loess Plateau of China – H Tian – PLoS One

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata. – M Gllart – Microbial Ecology

Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.). – ZF Yan – Int. J. Syst. Evol. Microbiol.

Water microbiome and extremophile

Microbial ecological associations in the surface sediments of Bohai strait – B Wang – Chinese Journal of Oceanology and Limnology

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. – PJ Gainer – PLoS One

Built environment

Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: key process parameters and microbial indicators of process instability – J Lee – Bioresource Technology

Phages and viruses

Temperate phages as frequency-dependent weapons in bacterial competition – XY Li – bioRxiv

Techniques

A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network. – S Zou – PLoS One

Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome – SF Rahman – bioRxiv

Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. – C Agrimonti – Critical Reviews in Food Science and Nutrition

Identification of regulatory targets for the bacterial Nus factor complex – G Baniulyte – bioRxiv

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study – S Langevin – The Journal of General Virology

Infection via mosquito bite alters Zika virus replication kinetics in rhesus macaques – D Dudley – bioRxiv

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1 – F Mauffrey – bioRxiv

Microbes in the news

Mimicry: by gut bacteria metabolites – Nutra Ingredients

Bacterial ‘aphrodisiac’ sends single-celled organism into mating frenzy – Nature News

Bacteria Use Brainlike Bursts of Electricity to Communicate – Quanta Magazine

Bacteria in Children’s Throats Found Strongly Associated with Bone and Joint Infections – Geneng News

How Farmers Can Help Ensure That We Don’t All Die From Super-Powered Bacteria – Fast Company

Harvey’s Floodwaters Contaminated With Nasty, Dangerous Bacteria – Houston Press

FOR THE FIRST TIME, GUT BACTERIA HAS BEEN SPOTTED EATING CHEMICALS IN THE BRAIN – Collective Evolution

University of Idaho research may slow antibiotic resistance to drugs – The Spokesman

September 5, 2017

Posted on September 5, 2017 by JP Cardenas

Jobs

Postdoctoral fellow in genomics of uncultured microbial parasites (SciLifeLab, Sweden) via Science Careers

Call for Assistant Professors and Professors (IST Austria, including for Life Sciences) via Science Careers

Human Microbiome

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection – Monica Di Paola – Scientific Reports

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy S.W. Wong – Microbiome (BMC)

Influence of Pregnancy History on the Vaginal Microbiome of Pregnant Women in their First Trimester – Dimitrios Nasioudis – Scientific Reports

Gut microbiome in ADHD and its relation to neural reward anticipation – Esther Aarts – PLoS ONE

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children – Shreyas V. Kumbhare – Scientific Reports

Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine – Hailong Cao – Scientific Reports

Review article: the human intestinal virome in health and disease – S. R. Carding – Alimentary Pharmacology and Therapeutics

Review: Organ-specific protection mediated by cooperation between vascular and epithelial barriers – Ilaria Spadoni – Nature Reviews Immunology

Review: Microbiota of chronic diabetic wounds: ecology, impact and potential for innovative healing strategies – Sonia Gonçalves Pereira – Frontiers in Microbiology

Animal Microbiome

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer – Yimeng Li – Frontiers in Microbiology

High-fat diet increases pain behaviors in rats with or without obesity – Zongbin Song – Scientific Reports

Research Highlights: The microbiota maintains oxygen balance in the gut – Irene Vacca – Nature Reviews Microbiology

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets – Zhuang Chen – Frontiers in Microbiology

Dietary heme induces gut dysbiosis, worsens colitis and potentiates the development of adenomas in mice – Marco Constante – Frontiers in Microbiology

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – Virginie Lemieux-Labonté – Microbiome (BMC)

Environmental and Soil Microbiome

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy – Suvendu Das – Frontiers in Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria – Eveline M. van den Berg – Frontiers in Microbiology

Beneficial microbes

Lactobacillus casei BL23 produces microvesicles carrying proteins associated with its probiotic effect – Ana P. Domínguez Rubio – Frontiers in Microbiology

Probiotic mixture Golden Bifido prevents neonatal Escherichia coli K1 translocation via enhancing intestinal defense – Qing Zeng – Frontiers in Microbiology

Protective Effect of Akkermansia muciniphila against Immune-mediated Liver Injury in a Mouse Model – Wenrui Wu – Frontiers in Microbiology

Methods

Review: Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa W. Hugerth – Frontiers in Microbiology

Total rRNA-Seq analysis gives insight into bacterial, fungal, protozoal and archaeal communities in the rumen using an optimized RNA isolation method – Chijioke O. Elekwachi – Frontiers in Microbiology

Non-Microbiology picks

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis – Julien Tripette – PeerJ

September 2, 2017

Posted on September 2, 2017 by Kiran

General microbiome

Nutrient stoichiometry shapes microbial coevolution – ML Larsen – bioRxiv

Review: Interplay of innate lymphoid cells and the microbiota – L Britanova – Immunological Reviews

Human gut microbiome

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens – S Kim – Immunological Reviews

Animal experiments

Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet – E Azad – Beneficial Microbes

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – L Chi – Toxicological Sciences

Animal microbiome

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients – MC Hughey – PeerJ

Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus – Y Jiang – Chinese Journal of Oceanology and Limnology

Plant, root, and soil microbiome

Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action – MD Asemoloye – PLoS One

Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil – AK Borsodi – International Journal of Systematic and Evolutionary Microbiology

Water microbiome and extremophiles

Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake – A Naghoni – International Journal of Systematic and Evolutionary Microbiology

Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum – S Woo – PLoS One

Biogeochemical conversion of sulfur species in saline lakes of Steppe Altai – SV Borzenko – Chinese Journal of Oceanology and Limnology

Role of heavy metals in structuring the microbial community associated with particulate matter in a tropical estuary – VA Sheeba – Environmental Pollution

Probiotics / prebiotics

Review: To add or not to add probiotics to infant formulae? An updated systematic review – A Skórka – Beneficial Microbes

Phages and viruses

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome – GD Hannigan – bioRxiv

Review: Impact of transmission cycles and vector competence on global expansion and emergence of arboviruses – A Agarwal – Reviews in Medical Virology

Techniques

Validation of RT-qPCR approaches to monitor Pseudomonas syringae gene expression during infection and exposure to pattern-triggered immunity – A Smith – bioRxiv

Review: Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – T Clavel – Immunological Reviews

Microbes in the news

Could an altered microbiome predict Parkinson’s disease – Nutra Ingredients

Could faecal microbiota transplantation be used to tackle asthma – Nutra Ingredients

Probiotics effective in preventing sepsis in infants – Healio

Start made on revealing scale of gut bugs’ hijacking our signalling – Chemistry World

Dietary Indoles May Help Extend Lifespan – Emax Health

Baby Bottle Soap Recalled Due to ‘Harmful Bacteria’ – Fortune

Multi-drug resistant bacteria proliferating through poultry waste – TOI

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Phages and viruses

September 29, 2017

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