Category Archives: Animal microbiome

January 30, 2018

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Today, the exposome on acne, eukaryotes in gut microbiota and chronic fatigue, oral and intestinal microbiome comparison in colorectal cancer, several studies in pathogen research, a review about rhizobia and more!

 

Human Microbiome

Short-Term Overfeeding with Dairy Cream Does Not Modify Gut Permeability, the Fecal Microbiota, or Glucose Metabolism in Young Healthy Men – Beate Ott – The Journal of Nutrition

The influence of exposome on acne – Brigitte Dréno – Journal of the European Academy of Dermatology and Venereology

Geographical Distribution and Diversity of Gut Microbial NADH:Ubiquinone Oxidoreductase Sequence Associated with Alzheimer’s Disease – Elena Paley – Journal of Alzheimer’s Disease

Book review: Microbiota in health and disease: from pregnancy to childhood in Beneficial Microbes

Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome – Alexandra H. Mandarano – PeerJ

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study – Edda Russo – Frontiers in Microbiology

Review: The Role of Skin and Orogenital Microbiota in Protective Immunity and Chronic Immune-Mediated Inflammatory Disease – Young Joon Park – Frontiers in Immunology

Short-Chain Fatty Acids Differentially Affect Intracellular Lipolysis in a Human White Adipocyte Model – Johan W. E. Jocken – Frontiers in Endocrinology

Year in Review: Cancer immunotherapy in 2017: The breakthrough of the microbiota – Guido Kroemer – Nature Reviews Immunology

 

Animal Microbiome

Sinus Microanatomy and Microbiota in a Rabbit Model of Rhinosinusitis – Do-Yeon Cho – Frontiers in Cellular and Infection Microbiology

EPSP of L. casei BL23 Protected against the Infection Caused by Aeromonas veronii via Enhancement of Immune Response in Zebrafish – Chubin Qin – Frontiers in Microbiology

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong – Ecology and Evolution

Exogenous Fecal Microbiota Transplantation from Local Adult Pigs to Crossbred Newborn Piglets – Luansha Hu – Frontiers in Microbiology

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity – Bing-Hong Huang – Frontiers in Microbiology

Hydrogen-water ameliorates radiation-induced gastrointestinal toxicity via MyD88’s effects on the gut microbiota – Hui-wen Xiao – Experimental & Molecular Medicine

Bacillus licheniformis normalize the ileum microbiota of chickens infected with necrotic enteritis – Shuai Xu – Scientific Reports

 

Beneficial Bacteria and Compounds

Review: Potential interactions among phenolic compounds and probiotics for mutual boosting of their health-promoting properties and food functionalities – A review – Evandro Leite de Souza – Critical Reviews in Food Science and Nutrition

Review: Impact of Dietary Fiber Consumption on Insulin Resistance and the Prevention of Type 2 Diabetes – Martin O Weickert – The Journal of Nutrition

Traditional Herbal Medicine-Derived Sulforaphene LFS-01 Reverses Colitis in Mice by Selectively Altering the Gut Microbiota and Promoting Intestinal Gamma-Delta T Cells – Ming Li – Frontiers in Pharmacology

Antimicrobial activity of apple cider vinegar against Escherichia coli, Staphylococcus aureus and Candida albicans; downregulating cytokine and microbial protein expression – Darshna Yagnik – Scientific Reports

 

Food Microbiome

Assertiveness of meat-borne Lactococcus piscium strains and their potential for competitive exclusion of spoilage bacteria in situ and in vitro – Maik Hilgarth – Journal of Applied Microbiology

 

Pathogen Research

Editorial: Do tetracyclines have the potential to reduce the risk of Clostridium difficile infection? – Sahil Khanna – Expert Review of Anti-infective Therapy

Minireview: Immunological roulette: Luck or something more? Considering the connections between host and environment in TB – John E Pearl – Cellular and Molecular Immunology

Review: Applications for Bacteriophage Therapy during Pregnancy and the Perinatal Period – Lucy L. Furfaro – Frontiers in Microbiology

Antibiotic-Induced Pathobiont Dissemination Accelerates Mortality in Severe Experimental Pancreatitis – Fernanda S. Soares – Frontiers in Immunology

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease – Karina Frahm Kirk – Scientific Reports

Exploration of the role of the virulence factor ElrA during Enterococcus faecalis cell infection – Natalia Nunez – Scientific Reports

 

Environmental Microbiome

Review: Rhizobia: from saprophytes to endosymbionts – Philip Poole – Nature Reviews Microbiology

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota – Nanna B Svenningsen – The ISME Journal

 

Microbiology – Other

News and Analysis: Genome watch: Keeping tally in the microbiome – Alexandre Almeida – Nature Reviews Microbiology

 

Non-microbiology picks

A meta-analysis of the diagnostic sensitivity and clinical utility of genome sequencing, exome sequencing and chromosomal microarray in children with suspected genetic diseases – Michelle M Clark – BioRxiv

January 29, 2018

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An exciting fellowship in Ireland, along with some interesting techniques in today’s digest!

Events and jobs
APEX (APC Postdoctoral EXcellence) Fellowship – Ireland
Fellowships will be offered in the four thematic APC research areas of ‘Microbes to Molecules’, ‘Diet and Microbes at the Extremes of Life’, ‘Brain-Gut-Microbiota Axis’ and ‘Host-Microbe Dialogue’. Adhering to the MSCA principle of ‘individual-driven mobility’.

Multi-site human microbiome
Review: Rethinking Antimicrobial Prophylaxis in the Transplant Patient in the World of Emerging Resistant Organisms-Where Are We Today? – Lucy E Horton – Current Hematologic Malignancy Reports

Human gut microbiome
Metabolic mechanisms of interaction within a defined gut microbiota – Gregory Leonard Medlock – bioRxiv

Gastric bacterial flora in patients harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – Bmc Gastroenterology

Review: Molecular Paths linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections – M Serino – Journal of Molecular Biology
(DOI not availabe yet, linked to PubMed)

Animal microbiome
Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity – Julie Reveillaud – Microbiome

Microbiome structure influences infection by the parasite Crithidia bombi in bumble bees – Blair K Mockler – Applied And Environmental Microbiology

Plant, root, and soil microbiome
The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C A Mallon – The Isme Journal

Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades – Hee-Sung Bae – Applied And Environmental Microbiology

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence – Jia Liu – Microbiome

Water and extremophile microbiome
Bioavailability of mineral-bound iron to a snow algae-bacteria co-culture and implications for albedo-altering snow algae blooms – Z R Harrold – Applied And Environmental Microbiology

Built environment
Structure, variation, and assembly of the deterioration-associated microbiome of stone monuments – Qiang Li – Applied And Environmental Microbiology

Targeting Bacteria and Methanogens to Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure – Jemaneh Habtewold – Applied And Environmental Microbiology

Techniques
Novel method reveals a narrow phylogenetic distribution of bacterial dispersers in environmental communities exposed to low hydration conditions. – U S Krüger – Applied And Environmental Microbiology

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. – Garold Fuks – Microbiome

Microbes in the news
What To Do If You Are Worried About Flesh Eating Bacteria – Bruce Y. Lee – Forbes

Be aware: Certain bacteria may increase HIV risk for women – Hindustan Times (see yesterday’s post for the paper in from Lancet Infectious Diseases)

New Astronaut Food Recipe Combines Human Waste and Bacteria – Jonathan Kesh – Outer Places

‘Bug memories’ could help fight looming crisis – Jamie Morton – New Zealand Herald

January 28, 2018

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A preprint on the gut microbiome of few tribal groups in the Himalayan region; association between vaginal microbiota and HIV;   an integrative approach that encompasses  metatranscriptomics & fatty acid profiling to study the rumen microbiome during feeding;   environmental adaptation shapes the gut microbiota of Rhesus macaques;   microbiome of cactus rhizosphere;   news about uBiome; antibiotics;  and many more articles for today’s digest!

General microbiome

Review: Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome – S Sandoval-Motta – Archives of Medical Research

Multi-site human microbiome

The nasal microbiome mirrors and potentially shapes olfactory function – K Koskinen – Scientific Reports

Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls – Y Qiao – Scientific Reports

Human respiratory microbiome

Pseudomonas aeruginosa Biofilms: Host Response and Clinical Implications in Lung Infections – NM Maurice – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Analysis of the skin mycobiome in adult patients with atopic dermatitis – SH Han – Experimental Dermatology

Human vaginal microbiome

Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study – RS McClelland – The Lancet

Prevalence of vaginal microorganisms among pregnant women according to trimester and association with preterm birth – K-A Son – Obstetrics & Gynecology Science

Human gut microbiome

Preprint: Gut microbiome transition across a lifestyle gradient in Himalaya – AR Jha – bioRxiv

Physical exercise, gut, gut microbiota, and atherosclerotic cardiovascular diseases – J Chen – Lipids in Health and Disease

Therapeutic Opportunities in Intestinal Microbiota–Virus Interactions – V Monedero – Trends in Biotechnology

Almond Consumption and Processing Affects the Composition of the Gastrointestinal Microbiota of Healthy Adult Men and Women: A Randomized Controlled Trial. – HD Holscher – Nutrients

Effects of Ampicillin on the Gut Microbiome of an Adult Male as Determined by 16S rRNA V4 Metagenomics Sequencing and Greengenes Bioinformatics Suite – K Anukam – Journal of Advances in Microbiology

Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis – EJ Laserna-Mendieta – Journal of Crohn’s and Colitis

The Role of Bacteria, Probiotics and Diet in Irritable Bowel Syndrome – A Harper – Foods

Animal experiments 

Preprint: Inter- and intra-domain functional redundancy in the rumen microbiome during plant biomass degradation – A Soellinger – bioRxiv

Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis. – N Jiao – Physiological Genomics

Protective effect of rosmarinic acid and carnosic acid against streptozotocin-induced oxidation, glycation, inflammation and microbiota imbalance in diabetic rats. – J Ou -Food & Function

Glucocorticoids Drive Diurnal Oscillations in T Cell Distribution and Responses by Inducing Interleukin-7 Receptor and CXCR4 – A Shimba – Immunity

Review: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – TT Nguyen – Journal of Psychiatric Research

Animal microbiome 

Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment – J Zhao – Microbial Ecology

Opinion: Mission Accomplished? We Need a Guide to the ‘Post Release’ World of Wolbachia for Aedes-borne Disease Control – SA Ritchie – Cell

Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster – KL Adair – The ISME Journal

In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor – YH Jo – Entomological Research

Plant, root and soil microbiome

Editorial special issue: the soil, the seed, the microbes and the plant – EB Nelson – Plant and Soil

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid – Y Zhang – Current Microbiology

The effects of road building on arbuscular mycorrhizal fungal diversity in Huangshan Scenic Area – A Yang – World Journal of Microbiology & Biotechnology

The role of species turnover in structuring bacterial communities in a local scale in the cactus rhizosphere – VN Kavamura – Plant and Soil

p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions – X Zhou – Biology and Fertility of Soils

Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition – M Unterseher – Mycological Progress

Identification, synthesis and regulatory function of the N-acylated homoserine lactone signals produced by Pseudomonas chlororaphis HT66 – H Peng – Microbial Cell Factories

Building Bioeconomy in Agriculture: Harnessing Soil Microbes for Sustaining Ecosystem Services – R Rengalakshmi – Towards a Sustainable Bioeconomy: Principles, Challenges and Perspectives

Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology – JL Wood – Frontiers in Microbiology

Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant – E Megías – Genome Announcements

Copper Bioleaching in China: Review and Prospect – S Yin – Minerals

Water microbiome and extremophiles 

Core promoter information content correlates with optimal growth temperature – AA Aptekmann – Scientific Reports

Food microbiology

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening – M Olvera-García – Applied Microbiology and Biotechnology

Phages and viruses

Review: Phage or foe: an insight into the impact of viral predation on microbial communities – L Fernández – The ISME Journal

Techniques

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity – KJ Hoegler – Journal of Molecular Evolution

Microbes in the news

uBiome, the Leader in Microbial Genomics, Launches SmartGut and SmartJane Microbiome Test Kits in Canada – Daily Telescope

Niki Bezzant: A gutsful of good health – NZ Herald

How Phenylbutazone, Firocoxib Affect Horses’ Gut Microbiota – the Horse

Botulinum-type toxins jump to a new kind of bacteria – Science Daily

‘Forgotten’ antibiotic offers hope against worst superbugs – Digital Journal

Detect The Level Of Bacteria In Food With This Smartphone-Based System – Wonderful Engineering

When bad bugs jump from farm to bedside – Hutch News

January 24, 2018

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General microbiome

Meta-analysis generates and prioritizes hypotheses for translational microbiome research – Claire Duvallet – microbial biotechnology

Resistance to Antibiotics: Are we prepared to Handle This Growing Ghost? – Ashima Kushwaha Bhardwaj – Omics Ebook Group

Pregnancy and early life

Neonate gut and respiratory microbiota: coordinated development through time and space – Alex Grier – bioRxiv

Human oral microbiome

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications – A. Mira – Advances in Dental Research (SAGE Journals)

Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols – L. Zhan – Advances in Dental Research (SAGE Journals)

The Caries Microbiome: Implications for Reversing Dysbiosis – A.C.R. Tanner – Advances in Dental Research (SAGE Journals)

In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P. D. Marsh – Advances in Dental Research (SAGE Journals)

Getting to Know “The Known Unknowns”: Heterogeneity in the Oral Microbiome – R. A. Burne – Advances in Dental Research (SAGE Journals)

Human gut microbiome

Adaptive Immune Education by Gut Microbiota Antigens – Qing Zhao – Immunology

Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Characterization of the fecal microbiota differs between age groups in Koreans – Sun-Young Kook – Intestinal Research

Diet, microbiota and inflammatory bowel disease: review – Bruna Luísa Radavelli – Nutrition & Food Science

The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori – Ingeborg Klymiuk – Frontiers in Microbiology

Gut Microbial Diversity in Women with Polycystic Ovary Syndrome Correlates with Hyperandrogenism – Pedro J Torres – JCEM

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls – Sudarshan A Shetty – bioRxiv

Animal experiments 

Modeling Host-Microbiome Interactions in Caenorhabditis elegans – Teklu K. Gerbaba – Journal of Nematology

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota – Zoya Alteber – Immunology & Cell Biology

A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols – Mei Cheng – Food & Function

Animal microbiome

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica – Juan G. Abarca – Frontiers in Microbiology

Functional Characteristics of the Flying Squirrel’s Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling – Hsiao-Pei Lu – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation – József Geml – New Phytologist

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

Assembly and ecological function of the root microbiome across angiosperm plant species – Connor R. Fitzpatrick – PNAS

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome – Jaderson Silveira Leite Armanhi – Frontiers in Plant Science

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function – Baneshwar Singh – Frontiers in Microbiology

Water and extremophile microbiome

Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O Roger Anderson – Frontier in Marine Science

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields – Teresa Cerqueira – Environmental Microbiology

Bioinformatics

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems – Ángel Martín Ortiz-Estrada – Reviews in Agriculture

[MSc Thesis] Optimizing the Reconstruction of Microbial Population Genomes from Metagenomes – Bhavya Nalagampalli Papudeshi – San Diego State University, ProQuest Dissertations Publishing

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Extension of the viral ecology in humans using viral profile hidden Markov models – Zurab Bzhalava – PLOS One

Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection – Karthika Suryaletha – International Wound Journal

A strategy for association study on intestinal microbiome and brain metabolome across lifespan of rats – Tianlu Chen – Analytical Chemistry

Techniques

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows – Jueeli D. Vaidya – Frontiers in Microbiology

Microbes in the news

Hyperandrogenism may alter gut microbiome in PCOS

Ed’s non-microbiology picks 

Using Fungi to Fix Bridges

Cooperating with machines – Jacob W. Crandall – Nature Communications

An investigation into the nutritional composition and cost of gluten-free versus regular food products in the UK – L. Fry – Journal of Human Nutrition and Dietetics

Prevalence and Trends in Prepregnancy Normal Weight — 48 States, New York City, and District of Columbia, 2011–2015 – CDC / Morbidity and Mortality Weekly Report

Exposed subsurface ice sheets in the Martian mid-latitudes – Colin M. Dundas – Science

Shorter sleep duration and longer sleep onset latency are related to difficulty disengaging attention from negative emotional images in individuals with elevated transdiagnostic repetitive negative thinking – Jacob A. Nota – Journal of Behavior Therapy and Experimental Psychiatry

January 23, 2018

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After the US government shutdown, today’s Digest features several human gut microbiome, food microbiology papers and many news pieces. There are some other highlights as well. A large longitudinal experiment in a tropical rain forest examines how soil microbes adapt genetically to nutrient changes in the soil. A synthetic enzyme rescues E. coli in iron-limited medium. Open access from high impact medical journals is still lacking.

Jobs and events

Digital Communications Officer – Microbiology Society – London

Keystone Symposium on Natural Products and Synthetic Biology

General microbiology

Sequence-based classification and identification of Fungi – David Hibbett et al. – Mycologia

Preprint: E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li et al. – bioRxiv

* A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli – Ann E Donnelly et al. – Nature Chemical Biology

Press: A randomly generated, totally novel enzyme rescues mutant bacteria – Diana Gitig – ArsTechnica

Annotations of Microbacterium foliorum – Debbie Jacobs-Sera – Sea Phages

Human gut microbiome

Reoccurring review (no abstract available): Letter to the Editor: Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Andre Alonso Taco-Masias and Augusto Rafael Fernandez-Aristi – Obesity Surgery

Also see a previous review: Influence of intestinal microbiota on body weight gain: a narrative review of the literature – Camila S. Cardinelli et al. – Obesity Surgery

Impact of intestinal mannitol on hyperammonemia, oxidative stress and severity of hepatic encephalopathy in the ED – Daniel H. Montes-Cortés et al. – The American Journal of Emergency Medicine

Clostridial strain-specific characteristics associated with necrotizing enterocolitis – Sophia Schönherr-Hellec et al. – Applied and Environmental Microbiology

Intestinal dysbiosis and permeability: the yin and yang in alcohol dependence and alcoholic liver disease – Peter Stärkel et al. – Clinical Science

In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way – Thaisa MoroCantu-Jungles et al. – Carbohydrate Polymers

Animal microbiome

In vitro: Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure – E.G. Ozbayram et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

* Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil – Qiuming Yao et al. – Nature Ecology and Evolution

Press: Researchers reveal how microbes cope in phosphorus-deficient tropical soil – Sara Shoemaker – Phys.org

Water and extremophile microbiome

Bacterial community changes in copper and PEX drinking water pipeline biofilms under extra disinfection and magnetic water treatment – J. Inkinen et al. – Journal of Applied Microbiology

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – M. Salomez et al. – Journal of Applied Microbiology

Lead-resistant bacteria from Saint Clair River sediments and Pb removal in aqueous solutions – Nichole Bowman et al. – Applied Microbiology and Biotechnology

Food microbiology

Ultrasound improves antimicrobial effect of sodium dichloroisocyanurate to reduce Salmonella Typhimurium on purple cabbage – Ana Lúcia Almeida Duarte et al – International Journal of Food Microbiology

Characterization of the spoilage potential of pure and mixed cultures of bacterial species isolated from tropical yellowfin tuna (Thunnus albacares) – A. Silbande et al. – Journal of Applied Microbiology

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year – L.M. Broissin-Vargas et al. – Journal of Applied Microbiology

An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England – C. Willis et al. – Journal of Applied Microbiology

Microbes in the news

Bacteria warning for Kapiti waterways – Newshub

Common salt kills rat fever bacteria? Public health experts say it can – TNN – Times of India

Editorial: Vendors’ ultimatum will save us from cholera, typhoid – The Standard

Why Flesh-Eating Bacteria Can Look Like the Flu – Rachael Rettner – Live Science

Geologists find bacteria that takes traces of gold and turns them into nuggets – Eliza Goetze – ABC News

Shigella Bacteria Diarrhea in Children: Should WHO Guidelines Be Modified? – Julie McShane – Medical News Bulletin

* Chemical ‘aphrodisiac’ jumpstarts the sex life of a single-celled organism – Brianna Abbott – Science Line

Microbiome predicts blood infections in pediatric cancer patients – EurekAlert

Dietary Fiber Protects Against Obesity and Metabolic Syndrome, Study Finds – Georgia State University News Hub

How climate change weakens coral ‘immune systems’ – EurekAlert

* Early changes in brain immunity may underlie sex bias in autism – Nicholette Zeliadt – Spectrum

Detecting Zoonotic Protists In Raw Sewage For Environmental Monitoring – Steven Sullivan – Science Trends

Microbes on the market

Synspira Therapy Eliminates Antibiotic-resistant Lung Bacteria, Study Shows – Marta Figueiredo – Cystic Fibrosis News Today

Microbiome Sequencing Service Market – Baseclear, Clinical-Microbiomics, MR DNA (Molecular Research Lp), Molzym, Zymo Research, Rancho Biosciences, Microbiome Therapeutics, Microbiome Insights, Openbiome, Resphera Biosciences, Shanghai Realbio Technology – Oscar – Hugo Press

VALBIOTIS Announces a Significant Effect of VALEDIA® on Intestinal Microbiota – Business Wire

Publishing and education

* Preprint: Open access policies of high impact medical journals: a cross-sectional study – Time Ellison et al. – bioRxiv

 

January 20, 2018

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Our Saturday digest has microbes associated with oesophageal region; sore throat; aphids, stingless bees; common carps, Italian cheeses and many more!

General microbiome

Bipartite network analysis of gene sharings in the microbial world – Eduardo Corel –

FEMS Microbiology Ecology

Is the impact of starvation on the gut microbiota specific or unspecific to anorexia nervosa? A narrative review based on a systematic literature search – Isabelle Mack – Current Neuropharmacology

Pregnancy and early life

Association between sn-2 fatty acid profiles of breast milk and development of the infant intestinal microbiome – Teimin Jiang – Food and Function

Multi-site human microbiome

The microbiology and treatment of human mastitis. – A Angelopoulou – Medical Microbiology and Immunology

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – PLoS Pathogens

Analysis of the tonsillar microbiome in young adults with sore throat reveals a high relative abundance of Fusobacterium necrophorum with low diversity – T. Preskott Atkinson – PLoS One

Human gut microbiome

Diet Affects Gut Microbiota and Modulates Hospitalization Risk Differentially In an International Cirrhosis Cohort – JS Bajaj – Hepatology

Emerging Insights into the Esophageal Microbiome – M May – Current Treatment Options in Gastroenterology

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study –  Y Shen – Schizophrenia Research

Animal experiments 

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – PLoS One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition & Food Research

Sequential BMP7/TGF-β1 signaling and microbiota instruct mucosal Langerhans cell differentiation. – Tal Capucha – Journal of Experimental Medicine

A host-pathogen interaction screen identifies ada2 as a mediator of Candida glabrata defences against reactive oxygen species – I Kounatidis – bioRxiv

Animal microbiome 

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts  – Nikoletta Geltsch – PLoS One

Stingless Bee Larvae Require Fungal Steroid to Pupate. – Camila R. Paludo – Scientific Reports

Plant, root and soil microbiome

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn – Claudia Y. Muñoz-Moreno – Genome Announcements

Biotic elicitation of ginsenoside metabolism of mutant adventitious root culture in Panax ginseng – Kim-Cuong Le – Applied Microbiology and Biotechnology

Streptomyces AcH 505 triggers production of a salicylic acid analogue in the fungal pathogen Heterobasidion abietinum that enhances infection of Norway spruce seedlings – Nadine Keilhofer – Antonie van Leeuwenhoek

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria – AS Sánchez-López – International Journal of Molecular Sciences

Extreme rainfall affects assembly of the root-associated fungal community – CJ Barnes – The New Phytologist

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. – BK Harrison – Geobiology

Review: Fungal-Mediated Solid Waste Management: A Review –  A Jain – Mycoremediation and Environmental Sustainability

The PEG-responding desiccome of the alder microsymbiont Frankia alni – K Ghedira – Scientific Reports

Composition of pelagic microbial communities in Mediterranean coastal aquatic ecosystems under extreme drought conditions – N Àvila –  Estuarine, Coastal and Shelf Science

Water microbiome and extremophile 

What color should glacier algae be? – Roman J dial – FEMS Microbiology Ecology

Microbial Community Structure of Sea Spray Aerosols at Three California Beaches – Katherine Graham – FEMS Microbiology Ecology

The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring – Dimitri Kalenitchenko – Scientific Reports

Microbial communities and their predicted metabolic functions in a desiccating acid salt lake – Elena Zaikova – Extremophiles

Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome – A Kumar – Seminars in Cell & Developmental Biology

Built environment 

Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells – Paolo Dessi – RSC Advances

Food microbiology

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses – Fabrizia Tittarelli – Microbial Genomics

Application of molecular tools to elucidate the microbiota of seafood – Paloma Almeida Rodrigues – Journal of Applied Microbiology

Review: Recent Past, Present, and Future of the Food Microbiome – Francesca De Filippis – Annual Review of Food Science and Technology

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional-omics – L Liu – Journal of Agricultural and Food Chemistry

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Q Li – Food Microbiology

Phages and viruses

Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – BG Blasdel – bioRxiv

Single-cell transcriptional dynamics of flavivirus infection – F Zanini – bioRxiv

Techniques

A distance-based approach for testing the mediation effect of the human microbiome – J Zhang – Bioinformatics

ReprDB and panDB: minimalist databases with maximal microbial representation – W Zhou – Microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – B LaSarre – bioRxiv

Microbes in the news 

WEBINAR REVIEW: IMMUNO-ONCOLOGY AND THE MICROBIOME – Taconic

Scientists Peek Inside The ‘Black Box’ Of Soil Microbes To Learn Their Secrets – npr

Broadways Nursing Home: Legionella bacteria found in plumbing – BBC

Agros refuses Troodos water after coliform bacteria found – Cyprus Mail Online

Strange Weather Triggered Bacteria That Killed 200,000 Endangered Antelope – npr

Bacterial biofilm cellulose found to differ from plant cellulose – Phys.org

This is what happens to your gut when you go on a juice cleanse – Well and Good

New Course in Virus Hunting – SDSU NewsCenter

January 19, 2018

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Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

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

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

January 18, 2018

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Today’s digest has quite a few reviews in “Human Gut Microbiome” section and quite interesting news: what killed Aztecs, the womb might not be sterile, while surfers might be spreading antibiotic-resistant bacteria. Check as well an interesting blog post on “How can academia kick its addiction to the impact factor?” and news about “Dimensions” – new science search engine. Dimensions not only indexes papers and their citations, but also – uniquely among scholarly databases – connects publications to their related grants, funding agencies, patents and clinical trials.

 

 

General microbiome

Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli – Nicole L Podnecky – bioRxiv

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – PLOS Computational Biology

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital – Claire L Gorrie – Clinical Infectious Diseases

Microbiological and molecular characterization of thermophilic Streptomycesvariabilis with antimicrobial activity – Ramy Fikry – Journal of Basic and Environmental Sciences

Population level evidence for seasonality of the human microbiome – Christina Korownyk – Chronobiology International

Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design –  Jacob W. Metch – Nature Nanotechnology

Microbial Competition of Rhodotorula mucilaginosa UANL-001L and E. coli increase biosynthesis of Non-Toxic Exopolysaccharide with Applications as a Wide-Spectrum Antimicrobial – Augusto Vazquez-Rodriguez – Scientific Reports

Pregnancy and early life

Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type – Min-Jung Lee – Journal of Allergy and Clinical Immunology

Overweight and obesity status in pregnant women are related to intestinal microbiota and serum metabolic and inflammatory profiles – Noora Houttu – Clinical Nutrition

Human respiratory microbiome

Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples – Nerea Abrego – Molecular Ecology Resources

Fungi stabilize connectivity in the lung and skin microbial ecosystems – Laura Tipton – BMC Microbiome

Oral microbiome

Microbiome associated with denture malodour – S Yitzhaki – Journal of Breath Research

High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation – Rafael Guerrero-Preston – Oncotarget

Location-Specific Oral Microbiome Possesses Features Associated With CKD – Jianzhong Hu – Kidney International Reports

Oral microbiota reduce wound healing capacity of epithelial monolayers, irrespective of the presence of 5-fluorouracil – Eline Vanlancker – Experimental Biology and Medicine

An experimental study for rapid detection and quantification of endodontic microbiota following photo-activated disinfection via new multiplex real-time PCR assay – Maryam Pourhajibagher – Photodiagnosis and Photodynamic Therapy

Review: Genome analysis and clinical implications of the bacterial communities in early biofilm formation on dental implants restored with titanium or zirconia abutments –  Flávia Correa Raffaini – Biofueling

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human nearly-sterile sites

The Microbiome and Neurologic Disease: Past and Future of a 2-Way Interaction – Javier Ochoa-Repáraz – Neurotherapeutics

Human gut microbiome

Mini Review: Beneficial actions of microbiota-derived tryptophan metabolites – J. J. Galligan – Neurogastroenterology & Motility

Review: Gut microbiome influences on anastomotic leak and recurrence rates following colorectal cancer surgery – S. Gaines – BJS

Review: Microbiota Signaling Pathways that Influence Neurologic Disease – Laura M. Cox – Neurotherapeutics

Review: How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota – Grégory Dubourg – Expert Review of Proteomics

Concise Review: Gut microbiota and probiotics: novel immune system modulators in myasthenia gravis? – Elena Rinaldi – Annals of the New York Academy of Science

Research Highlights: Gut microbiota: Targeting of specific microbial species mitigates colitis – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology

Research Highlights: Gut microbiota: Filling up on fibre for a healthy gut – Katrina Ray – Nature Reviews Gastroenterology and Hepatology

Stachyose Improves Inflammation Through Modulating Gut Microbiota of High-Fat Diet / Streptozotocin Induced Type 2 Diabetes in Rats – Guimei Liu – Molecular Nutrition & Food Research

Analysis of fecal microbiota in patients with functional constipation undergoing treatment with synbiotics – Lin Sheng Huang – European Journal of Clinical Microbiology & Infectious Diseases

The microbiota metabolite indole inhibits Salmonella virulence: Involvement of the PhoPQ two-component system – Nandita Kohli – PLOS

Metatranscriptome of human faecal microbial communities in a cohort of adult men – Galeb S. Abu-Ali – Nature Microbiology

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Li-Juan Qian –

Animal experiments

Impact of Trans-Fats on Heat-Shock Protein Expression and the Gut Microbiota Profile of Mice – Gessika Cristina Borges Castro Carvalho – Journal of Food Science

Animal microbiome 

The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome – J. A. Rubiolo – Antonie van Leeuwenhoek

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Interactions Between Parasites and the Bacterial Microbiota of Chickens – Rüdiger Hauck – Avian Diseases

Plant, root, and soil microbiome

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMS Microbiome

Saving seed microbiomes – Gabriele Berg – The ISME

Rice Crop Growth and Rhizospheric Microbial Dynamics in Heavy Metals Contaminated Inceptisol – Manoj Shrivastava – Water Quality Management

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMC Microbiome

Water and extremophile microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – Breah LaSarre – bioRxiv

Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism – Alexander J Probst – bioRxiv

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael Winslow Henson -bioRxiv

Data Descriptor: The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans – Benjamin J. Tully – Scientific Data

Survey of sulfur-oxidizing bacterial community in the Pearl River water using soxB, sqr, and dsrA as molecular biomarkers – Jianfei Luo – 3 Biotech

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes – J. Keshri – Microbial Ecology

Coral physiology and microbiome dynamics under combined warming and ocean acidification – Andréa G. Grottoli – PLOS

Crenothrix are major methane consumers in stratified lakes – Kirsten Oswald – The ISME

 

Food microbiology

Review: Modern perspectives on the health benefits of kefir in next generation sequencing era: improvement of the host gut microbiota – Dong-Hyeon Kim –  Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Lactobacillus acidophilus Improves Intestinal Inflammation in an Acute Colitis Mouse Model by Regulation of Th17 and Treg Cell Balance and Fibrosis Development – Park Jin-Sil – Journal of Medicinal Food

Phages and viruses

Interferons: Reprogramming the Metabolic Network against Viral Infection – Kavita Raniga  – Viruses

Bioinformatics

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data – Saima Sultana Tithi – PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Jie Ren – BMC Microbiome

Techniques

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – BMC Microbiome

Microbes in the news

500 years later, scientists discover what probably killed the Aztecs

Could baby’s first bacteria take root before birth?

Robotic baby helps researchers understand how biological dust develops immunity in crawling babies

Surfers May Be Spreading Antibiotic-Resistant Bacteria From Swallowing Poop-Laced Water

Microbes and Art

Artist Hunter Cole Presents Exhibit Featuring Photos of Bacteria That Create Their Own Light

Science, publishing, and career 

Science search engine links papers to grants and patents

How can academia kick its addiction to the impact factor?

 

January 17, 2018

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In today’s digest, a review of the skin microbiome and a brilliant article on role of microbes in plant speciation. Lastly, the microbiome of the ever impressive water bear.

General Microbiome

Editorial: Special Issue on ‘Microbe-host interactions’.Hammerschmidt S. FEBS Letters.

Review: The stress concept in gastroenterology: from Selye to today.Elsenbruch S. F1000 Research

Review:Role of human microbiome and selected bacterial infections in the pathogenesis of rheumatoid arthritis. Roszyk E. Reumatologia

Gut Microbiome

Review: Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation.Akkerman R. Critical Reviews in Food Science and Nutrition

Review: Diet, Gut Microbiota, and Colorectal Cancer Prevention: A Review of Potential Mechanisms and Promising Targets for Future Research.Song M. Current Colorectal Cancer Reports

Skin Microbiome

Review: The human skin microbiome. Byrd AL. Nature Reviews Microbiology

Anal Microbiome

Is there a link between aging and microbiome diversity in exceptional mammalian longevity? Hughes GM. PeerJ

Plant, Soil, and Water Microbiome

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation.Geml J. New Phytologist.

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective.VanMensel D. Microbial Ecology

Animan Experiments and Microbiome

The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition.Vecchi M, Newton ILG, Cesari M. Microbial Ecology

Peracetic acid disinfection kinetics for combined sewer overflows: indicator organisms, antibiotic resistance genes, and microbial community.Eramo A. Environmental Science: Water Research and Technology

Protocol

Oral Microbiome Characterization in Murine Models. Abusleme L. Bio-protocol

Microbes in the NEWS

Can Probiotics Improve the Gut Flora and Reduce Complications after Surgery?

-Medical News Bulletin

 

January 16, 2018

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Today, a set of interesting papers about the stability of human microbiome, ancient genomes from XVI Century Salmonella strains, a nice review about human skin microbiome, antimicrobial resistance genes in the International Space Station and more!

 

Human Microbiome

Stability of the human faecal microbiome in a cohort of adult men – Raaj S. Mehta – Nature Microbiology

Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation – Renate Akkerman – Critical Reviews in Food Science and Nutrition

Review: The human skin microbiome – Allyson L. Byrd – Nature Reviews Microbiology

The Relationship between Habitual Dietary Intake and Gut Microbiota in Young Japanese Women – Takahiro Seura – Journal of Nutritional Science and Vitaminology

Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy – Casey Chen – The ISME Journal

Cigarette smoking is associated with an altered vaginal tract metabolomic profile – T. M. Nelson – Scientific Reports

Review: Infectious Agents and Inflammation: The Role of Microbiota in Autoimmune Arthritis – Andrea Picchianti-Diamanti – Frontiers in Microbiology

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study – Edda Russo – Frontiers in Microbiology

 

Animal Microbiome

Fosfomycin residues in colostrum: Impact on morpho-physiology and microbiology of suckling piglets – M.B. Fernández Paggi – Journal Of Veterinary Pharmacology And Therapeutics

The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition – Matteo Vecchi – Microbial Ecology

Oral Microbiome Characterization in Murine Models – Loreto Abusleme – Bio-Protocol

Corallivory and the microbial debacle in two branching scleractinians – Yvan Bettarel – The ISME Journal

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in Microbiology

 

Built Microbiome

Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces – C. Urbaniak – Scientific Reports

 

Plant and Environmental Microbiome

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence – Francesca Mapelli – The ISME Journal

Perspective: Saving seed microbiomes – Gabriele Berg – The ISME Journal

Preprint: Microbial biogeography of 1,000 geothermal springs in New Zealand – Jean F Power – Biorxiv

 

Pathogen Research

Effect of outpatient antibiotics for urinary tract infections on antimicrobial resistance among commensal Enterobacteriaceae: a multinational prospective cohort study – Andrew J. Stewardson – Clinical microbiology and infection

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico – Åshild J. Vågene – Nature Ecology & Evolution

Bovine Lactoferrin and Lactoferrin-Derived Peptides Inhibit the Growth of Vibrio cholerae and Other Vibrio species – Erika Acosta-Smith – Frontiers in Microbiology

 

General Microbiome

The stress concept in gastroenterology: from Selye to today – Sigrid Elsenbruch – F1000Reseach

Review: Deoxynivalenol, gut microbiota and immunotoxicity: A potential approach? – Yuxiao Liao – Food and Chemical Toxicology

Research Highlight: Anti-PD1 in the wonder-gut-land – Marie Vetizou – Cell Research

 

Other

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways – Diana Z. Sousa – Nature Communications

Preprint: Conserved mass peaks in MALDI-TOF mass spectra of bacterial species – Wenfa Ng – PeerJ