June 10, 2017

Jobs and events

Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota

Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM

 

General microbiome

Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics

Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology

Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology

 

Human gut microbiome

Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model –  N Yin – Chemosphere

Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review

 

Animal experiment

A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy

 

Animal microbiome

Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development

 

Plant, root and soil microbiome

The nodule microbiome; N2-fixing rhizobia do not live alone  – P  Martínez-Hidalgo – Phytobiomes Journal

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology

Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry

Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology

 

Water microbiome and extremophile

Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica

Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research

 

Techniques

Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv

Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy

 

Metabolomics

Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla –  F Gu – AMB Express

 

Phages

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics

 

Built environment microbiome

Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv

Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research

 

More microbes

Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses

Protozoa and microbiome  – SL Burgess – Infection and Immunity

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens  – JE Heindl – bioRxiv

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv

 

Microbes in news

Engineering ‘good’ bacteria to kill bad ones – The Straits Times

White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos

Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire

New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism

Therapy could stop superbugs on farms – P Ghosh – BBC News

SHU students travel to present phages research – P Parise – Setonian Online

June 9, 2017

Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today

June 4, 2017

Some exciting papers in the sections- General microbiome & Microbes in news, to get you through Sunday!

General microbiome

The 5D Framework: A Clinical Primer for Fecal Microbiota Transplantation to Treat Clostridium difficile infection – JR Allegretti – Gastrointestinal Endoscopy

Abatement of AO7 in a divided microbial fuel cells by sequential cathodic and anodic treatment powered by different microorganisms – G Riccobono – Journal of Electroanalytical Chemistry

THE MICROBIOME AND TRANSFUSION IN CANCER PATIENTS – H Goubran – Transfusion and Apheresis Science

« Olsenella congonensis» sp.nov., identified in human stool sample – M Bilen – New Microbes and New Infections

Description of “Blautia phocaeensis” sp.nov., and “Lachnoclostridium edouardi” sp. nov., isolated from healthy fresh stools of Saudii Arabia bedouins by culturomics – SI Traore  – New Microbes and New Infections

Sulfur-driven iron reduction coupled to anaerobic ammonium oxidation – P Bao – Environmental Science and Technology

 

Animal microbiome

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – E Lobato – Symbiosis

Modulation of ruminal fermentation profile and microbial abundance in cows fed diets treated with lactic acid, without or with inorganic phosphorus supplementation – E Mickdam – Animal Feed Science and Technology

A pea (Pisum sativum L.) seed albumin extract prevents colonic DSS induced dysbiosis in mice – I Aranda-Olmedo – Journal of Functional Foods

 

Human respiratory microbiome

The Respiratory Microbiome: Beyond the Culture – E Monsó – Archivos de Bronconeumología

WS03.7 Coexistence of prey and predator bacteria in cystic fibrosis lung microbiota – J. de Dios-Caballero – Journal of Cystic Fibrosis

 

Human gut microbiome

The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner – P Ó Cuív – Anaerobe

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – M Vollmer – Food Research International

Consumption effect of a synbiotic beverage made from soy and yacon extracts containing Bifidobacterium animalis ssp. lactis BB-12 on the intestinal polyamine concentrations in elderly individuals – MSJ Manzoni – Food Research International

Review: Effect of diet and gut environment on the gastrointestinal formation of N-nitroso compounds: A review – J Kobayashi – Nitric Oxide

Atopic dermatitis and food sensitization in South African toddlers : Role of fiber and gut microbiota – M Mahdavinia – Annals of Allergy, Asthma & Immunology

 

Plant, root and soil microbiome

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome – JW Neilson – mSystems

Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure – SA Wood – Soil Biology and Biochemistry

The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens – W Xie – Applied Microbiology and Biotechnology

Relative roles of competition, environmental selection and spatial processes in structuring soil bacterial communities in the Qinghai-Tibetan Plateau – J Zhou – Applied Soil Ecology

Isolation and identification of endophytic bacteria with plant growth promoting and biocontrol potential from oak trees – F Tashi-Oshnoei – Forest Pathology

Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants – X Du – Probiotics and Antimicrobial Proteins

The influence of land use intensity on the plant-associated microbiome of Dactylis glomerata L. – J Estendorfer – Frontiers in Plant Science

 

Water microbiome and extremophiles

An overlooked nitrogen loss linked to anaerobic ammonium oxidation in estuarine sediments in China – XR Yang – Journal of Soils and Sediments

 

Food microbiology

Evolution of microbiota during spontaneous and inoculated Tonda di Cagliari table olives fermentation and impact on sensory characteristics – R Comunian – LWT-Food Science and Technology

PCR-DGGE markers for qualitative profiling of microbiota in raw milk and ripened cheeses – B Nalepa – LWT-Food Science and Technology

Identification of enzymatic activities involved in agave fructan consumption by Bifidobacterium longum subsp. infantis ATCC 15697 – E Cuevas-Juárez – Journal of Functional Foods

 

Techniques

Photodynamic Therapy With Methylene Blue for Skin Ulcers Infected With Pseudomonas aeruginosa and Fusarium spp – C Aspiroz – Actas Dermo-Sifiliográficas

 

Phages

Antibacterial efficacy of nisin, bacteriophage P100 and sodium lactate against Listeria monocytogenes in ready-to-eat sliced pork ham – ACL Figueiredo – Brazilian Journal of Microbiology

 

More microbes

Spore forming bacteria in beer: occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – ARG Munford – Food Control

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil – FF Vaz – Brazilian Journal of Microbiology

Species specific substrates and products choices of 4-O-acetyltransferase from Trichoderma brevicompactum – S Sharma – Enzyme and Microbial Technology

Review: The Goldilocks model of immune symbiosis with Mycobacteria and Candida colonizers – RT Robinson – Cytokine

Immunological and epidemiological factors affecting candidiasis in HIV patients beginning antiretroviral therapy in an Asian clinic – EAT Wulandari – Archives of Oral Biology

Diversity and Ecology of and Biomineralization by Magnetotactic Bacteria – W Lin – Environmental Microbiology Reports

 

Microbes in news

Man Dies After His Tattoo Gets Infected with Ocean Bacteria – R Rettner – Live Science

Accelerated breeding of mutant bacteria may choke space race – J Seidel – News Corp Australia Network

Microgravity Can Permanently Mutate Bacteria to Make Them Faster Breeders –  D Nield – Science Alert

Vaginal bacteria can inhibit sexual transmission of Zika virus – Healio

Bacteria levels subside, Spring Lake beach reopens – R Zimmer – App.com

Meet C. diff, the gross bacteria on the soles of your shoes – E Roberts – Today

The Microscopic World of Bacteria Comes to Life with Sculpture – CR  Fernández – Labiotech

New Microbiology Data Reinforce Activity of Paratek’s Omadacycline Against Pathogens of Importance in Respiratory, Skin and Urinary Tract Infections – Paratek – Nasdaq Globe News Wire

A Traumatic Experience Can Reshape Your Microbiome – S Neilson – Huffington Post

Zymo Research to Launch Three New Kits for Microbiome Research at ASM Microbe 2017 – Zymo Research Corp. – PR Newswire

The gut microbiota plays key role in diabetes treatment – N Marriott –  Drug Target Review

In a first, Human Microbiome Project Launched in Northeast India! – TNT News

Metformin joins forces with gut microbes to improve blood sugars, new study finds – C Bienvenu – Diabetes.co.uk

 

 

May 27, 2017

Today’s digest has some great papers in the section-Plant, root and soil microbiome

General microbiome

Concentration and Viability of Bacterial Aerosols Associated with Weather in Asian Continental Outflow: Current Understanding – D Zhang – Aerosol Science and Engineering

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture – H Li – bioRxiv

Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides – P Mergaert – Trends in Microbiology

Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts – N Filipowicz – Water, Air, & Soil Pollution

 

Animal microbiome

Impact of dietary Moringa oleifera leaves on intestinal pathogenic load and histological structure of growing rabbits raised under heat-stress conditions – AY El-Badawi – Animal Production Science

CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice – KN Chitrala – European Journal of Immunology

Meta-analysis To Define a Core Microbiota in the Swine Gut – DB Holman – mSystems

 

Plant, root and soil microbiome

Let the Core Microbiota Be Functional – P Lemanceau – Trends in Plant Science

Phytobiomes – Editor-in-Chief: CA Young

Bio-mining the forest ecosystem of North East India for identification of antimicrobial metabolites from fungi through submerged fermentation – SI Devi – Bioresource Technology

Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity – SL Svensson – mBio

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research – CE Stanley – Trends in Microbiology

Soil microbial properties as affected by short-term contrasting tillages and cropping systems in a rainfed agro-ecosystem of Northern Odisha – KN Mishra – Evolutionary Ecology

Comparison of rhizosphere properties as affected by different Bt- and non-Bt-cotton (Gossypium hirsutum L.) genotypes and fertilization – M Ahamd – Environmental Monitoring and Assessment

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity – T Yang – New Phytologist

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils – JD Castillo – Microbial Ecology

Lipopeptides produced by B. amyloliquefaciens NJN-6 altered the soil fungal community and non-ribosomal peptides genes harboring microbial community – J Yuan – Applied Soil Ecology

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web – P Harkes – Oikos

 

Food microbiology

Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes’ milk cheese – F Cardinali – International Journal of Food Microbiology

High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions – CJ Doyle – International Journal of Food Microbiology

 

Built environment microbiology

Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics – J Liao – Applied Microbiology and Biotechnology

 

Techniques

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium – R Kumar – mSystems

Fermentation quality, in vitro digestibility and aerobic stability of total mixed ration silages prepared with whole-plant corn (Zea mays L.) and hulless barley (Hordeum vulgare L.) straw – X Yuan – Animal Production Science

Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis – Y Zhou – International Biodeterioration & Biodegradation

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads – JM Maritz – Microbial Ecology

 

More microbes

HIV Persistence Alters CXCR4 Expression Patterns In OP9-DL1-Mediated Differentiation Of In Vitro Infected Human Cord Blood CD34+ Cells – T Tsukamoto – bioRxiv

Bacterial Virus Ontology; Coordinating across Databases – C Hulo – MDPI

 

Microbes in news

New insights into the ancestors of all complex life – University of Bristol – News

How a Usually Harmless Bacteria Ended Up Killing 18 People in Wisconsin – S Zhang – The Atlantic

Where you can check beaches for bacteria – Daily Herald

Beware: How to avoid rare flesh-eating bacteria in Chesapeake Bay – M Basch – WTOP

Gut Microbiome Affects Two Nervous System Diseases – AL Komarrof – Journal Watch

Solution to many global challenges may be right under our feet – G Dufficy – AgriLand

Bugging cancer: gut bacteria and the big C – V Martinez – The Irish Times

 

Non-microbiology picks

Marginal Returns And Levels Of Research Grant Support Among Scientists Supported By The National Institutes Of Health – MS Lauer – bioRxiv

Conservation and restoration practices in humid climates – D Tejeda Sartorius – CAB Direct

May 25, 2017

A review on the “vine and wine” microbiomes, a fungus that can infect and kill mosquitos through interaction with the gut microbiota, an introduction to the viruses of coral reefs.

General microbiome

The Role of Microbiota and Immunobiotics in Granulopoiesis of Immunocompromised Hosts – Susana Salva – Frontiers in Immunology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations – Felix Goldschmidt – The ISME Journal

Human gut microbiome

TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota – Sozaburo Ihara – Journal of Gastroenterology

Review: Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions – Mark N Read – Frontiers in Immunology

Review: Genes, emotions and gut microbiota: The next frontier for the gastroenterologist – Arturo Panduro – World Journal of Gastroenterology

Animal experiments

Modulation of the gut microbiota impacts non-alcoholic fatty liver disease: a potential role for bile acids – Aafke WF Janssen – Journal of Lipid Research

Antimicrobial peptides extend lifespan in Drosophila – Gerrit Loch – PLOS ONE

Animal microbiome

Bacterial diversity of cosmopolitan Culex pipiens and invasive Aedes japonicus from Germany – Sina Zotzmann – Parasitology Research

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria – Jan Hubert – Microbial Ecology

* Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality – Ge Wei – PNAS

Plant, root, and soil microbiome

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships – Isabelle Laforest-Lapointe – Nature

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – The ISME Journal

Review: From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept – Ignacio Belda – Frontiers in Microbiology

Phages and viruses

Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations – Maria A Bautista – Viruses

Review: Virus–host interactions and their roles in coral reef health and disease – Rebecca Vega Thurber – Nature Reviews Microbiology

Metabolomics

Inter-individual Recovery of the Microbiota and Metabolome Over Time Following Fecal Microbiota Transplantation in Patients with Recurrent Clostridium difficile Infection – Anna M Seekatz – bioRxiv

Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice – Daxesh P Patel – PLOS ONE

Review: Livestock metabolomics and the livestock metabolome: A systematic review – Seyed Ali Goldansaz – PLOS ONE

Techniques

Review: A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia – Antonella Succurro – Journal of Bacteriology

More microbes

Decoding and reprogramming fungal iterative nonribosomal peptide synthetases – Dayu Yu – Nature Communications

Microbes in the news

Companies Pursue Diagnostics that Mine the Microbiome – Andrea Anderson – The Scientist

The fungal microbiome contributes to alcohol-induced liver damage in mice – EurekAlert

May 11, 2017

Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.

General microbiome

Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE

Human oral microbiome

The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research

Human gut microbiome

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis

Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens

Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology

Animal experiments

* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature

* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS

Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research

Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports

Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports

Animal microbiome

* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications

Plant, root, and soil microbiome

Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE

Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology

Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry

The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology

Water and extremophile microbiome

Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews

Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv

Probiotics/prebiotics

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology

Bioinformatics

dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics

Techniques

Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine

Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology

Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE

More microbes

When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology

Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications

Microbes in the news

Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News

A defence mechanism that can trap and kill TB bacteria – Science Daily

Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek

Bacteria art

Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com

April 27, 2017

An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology

Probiotics/prebiotics

Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Bioinformatics

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports

Techniques

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature