January 28, 2018

Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv

January 25, 2018

Posted on January 25, 2018 by barnettburns

Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

*****************************

Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

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

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

*****************************

Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin – Food and Function

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

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

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

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

*****************************

Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

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

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

*****************************

Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

January 23, 2018

Posted on January 23, 2018 by xinhuang7

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 21, 2018

Posted on January 21, 2018 by Kiran

A light reading for Sunday!

Events and jobs

Professor (Chairperson), Department of Microbiology and Immunology (MIC) – The Uniformed Services University of the Health Sciences – Bethesda, Maryland

Postdoc in Intestinal Microbiology and Ecology – The National Food Institute (DTU Food) – Denmark

SCIENCE INQUIRY LECTURE: “FLYING” BACTERIA AS POTENTIAL RAINMAKERS – APRIL 18, 2018; 7:00PM – 8:30PM – HAGER AUDITORIUM, Montana

General microbiome

Review: Bacterial RNA Biology on a Genome Scale – Jens Hör – Molecular Cell

Multi-site human microbiome

Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye – Xiaofeng Wen – Progress in Retinal and Eye Research

Human skin microbiome

The role of fatty acids and their endocannabinoid-like derivatives in the molecular regulation of appetite – Renger F. Witkamp – Molecular Aspects of Medicine

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair – Jonathan L. Linehan – Cell

Propionibacterium acnes Strains Differentially Regulate the Fate of Th17 Responses in the Skin – Emmanuel Contassot – Journal of Investigative Dermatology

Human gut microbiome

P038 FECAL MICROBIOTA TRANSPLANT (FMT) FOR IMMUNO-CHECKPOINT INHIBITOR-INDUCED COLITIS (ICI-C) IN A 50 YEAR OLD FEMALE WITH BLADDER CANCER – Yinghong Wang – Gastroenterology

P110 STEROID-RESISTANCE AND STEROID-DEPENDENCE IN INFLAMMATORY BOWEL DISEASE CAN BE LINKED WITH GUT MICROBIOTA COMPOSITION CHANGES – Natalia Danilova – Gastroenterology

P069 LOW FAT DIET IMPROVES QUALITY OF LIFE AND CHANGES THE MICROBIOME IN A CATERED, CROSS-OVER DESIGN INTERVENTION OF UC PATIENTS WITH QUIESCENT DISEASE: RESULTS OF A PILOT STUDY – Matthew C. Phillips – Gastroenterology

Animal experiments

The family Coriobacteriaceae is a potential contributor to the beneficial effects of Roux-en-Y gastric bypass on type 2 diabetes – Haijun Liu – Surgery for Obesity and Related Diseases

P039 FECAL MIRNAS SHAPE THE INTESTINAL MICROBIOTA – Emilie Viennois – Gastroenterology

P125 TLR4 ACTIVATION UPREGULATES EXPRESSION OF OXIDATIVE ENZYMES: IMPLICATIONS FOR INTESTINAL TUMORIGENESIS AND LUMINAL MICROBIOTA – Juan F. Burgueno – Gastroenterology

Effect of live yeast supplementation on gastric ecosystem in horses fed a high-starch diet – Samy Julliand – Livestock Science

The symbiont Lactobacillus plantarum causes intestinal pathogenesis in adult Drosophila. – David Fast – bioRxiv

Plant, root and soil microbiome

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation – Chao Ai – Geoderma

Microbial degradation of poly(ε-caprolactone) in a coastal environment – Miwa Suzuki – Polymer Degradation and Stability

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape – Sergio E. Morales – Applied Soil Ecology

Food microbiology

Polyphasic identification of Penicillia and Aspergilli isolated from Italian grana cheese – Simone Decontardi – Food Microbiology

Phages and viruses

Bacteriophages as modulator for the human gut microbiota: Release from dairy food systems and survival in a dynamic human gastrointestinal model – Meike Samtlebe – LWT

Techniques

Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population – Prathik K Vijay Kumar – bioRxiv

P168 WHERE WILL FECAL MICROBIOTA TRANSPLANTATION FIT IN THE TREATMENT ALGORITHMS FOR CROHN’S DISEASE AND ULCERATIVE COLITIS: A SYNTHESIS OF COMPLETED, ONGOING AND FUTURE TRIALS – Yiran Song – Gastroenterology

Microbes in the news

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago – Mental Floss

IIT Delhi develops a novel platform to test drug sensitivity in bacteria – The Hindu

Scientists Unlock Key Information About the World’s Soil Microbes – Yale Environment 360

January 20, 2018

Posted on January 20, 2018 by Kiran

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 17, 2018

Posted on January 17, 2018 by Itumeleng

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 15, 2018

Posted on January 15, 2018 by Itumeleng

Today’s digest is full of great papers, including new methods of detection and quantificaion of HGT in anoxic conditions, and a brilliant paper on root-rhizosphere interactome.

General Microbiome

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Mateos, R. Bioelectrochemistry.

Gut Microbiome

Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Zhang Y. Molecular Nutrition Food Research

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients. Cui, X. Scientific Reports

Nasal Microbiome

An insight into intestinal mucosal microbiota disruption after stroke.Stanley,D. Scientific Reports

Influence of pig farming on the human’s nasal microbiota: The key role of the airborne microbial communities. Kraemer, JG. Applied and Environmental Microbiology

Fecal Microbiome

Letters to Editor: Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition. Thingholm L. Gut

Plant, Soil, and Water Microbiome

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. Yergeau, E. The ISME Journal

Indoor Microbiome

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.Raghupathi, PK. Applied and Environmental Microbiology

Resitome

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Shi, Y. Applied Microbioloby and Biotechnology

Animan Experiments and Microbiome

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. He, J. Scientific Reports

Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Khan, TJ. Scientific Reports

Protocol/Techniques

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments. Pinilla, R. Applied and Environmental Microbiology

Microbiome Jobs

Part-Time Microbiology Laboratory Technician

-Inside Higher Ed Careers

January 14, 2018

Posted on January 14, 2018 by Itumeleng

Today’s digest features brilliant ‘Letters to the Editors’ articles in response to recently published works, and concise microbiome reviews. Lastly, an improved method for assembly of functional metagenomes.

Gut Microbiome

Letters to the Editor: Navigating the Microbiota Seas: Triangulation Finds a Way Forward. Rosen, CE. Cell Host & Microbe.

Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type. Lee, M-J. Journal of Allergy and Clinical Immunology

Insect Microbiome

REVIEW: Functional roles and metabolic niches in the honey bee gut microbiota. Bonilla-Rosso, G. Current Opinion in Microbiology

Letters to the Editor: Insect Gut Microbiota: Accessories to the Bite. Aksoy, S. Cell Host & Microbe

Animal Experiments and Microbiome

Characterisation of the intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) fed with Hermetia illucens (black soldier fly) partially defatted larva meal as partial dietary protein source. Bruni, L. Aquaculture

REVIEW: Gastrointestinal tract (gut) health in the young pig. Pluske, JR. Animal Nutrition

Plant, soil, and water Microbiome

Deciphering the bacterial and fungal communities in clubroot-affected cabbage rhizosphere treated with Bacillus Subtilis XF-1. Liu, C. Agriculture, Ecosystems & Environment

REVIEW:Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review. Janzen dos Santos, J. Journal of Environmental Management.

Food Microbiome

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation. De Filippis. Food Microbiology

Techniques/Protocol

REVIEW: Fluorescence activated cell-sorting principles and applications in microalgal biotechnology. Pereira, H. Algal Research

A-GAME: improving the assembly of pooled functional metagenomics sequence data. Chiara, M. BMC Genomics

Microbes in the News

Research Says Exercise Also Improves Your Gut Bacteria

-Healthline

	Francis W on The Hetch Hetchy Railroad
	Best Practice Exchan… on June 1, 2018
	May 17, 2024 \| Micro… on May 15, 2024
	Kathy Brown on The Hetch Hetchy Railroad
	John Wilbur on The Hetch Hetchy Railroad

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

General microbiome

Multi-site human microbiome

Human respiratory microbiome

Human skin microbiome

Human vaginal microbiome

Human gut microbiome

Animal experiments

Animal microbiome

Plant, root and soil microbiome

Water microbiome and extremophiles

Food microbiology

Phages and viruses

Techniques

Microbes in the news

A Saturday digest with lots of fun and weird news of microbiome!

Events and jobs

General microbiome

Pregnancy and early life

Human gut microbiome

Animal experiments

Plant, root and soil microbiome

Water microbiome and extremophile

Food microbiology

Phages and viruses

Microbes in the news

A light reading for Sunday!

Events and jobs

General microbiome

Multi-site human microbiome

Human skin microbiome

Human gut microbiome

Animal experiments

Plant, root and soil microbiome

Food microbiology

Phages and viruses

Techniques

Microbes in the news

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

General microbiome

Pregnancy and early life

Multi-site human microbiome

Human respiratory microbiome

Human gut microbiome

Animal experiments

Animal microbiome

Plant, root and soil microbiome

Water microbiome and extremophile

Built environment

Food microbiology

Phages and viruses

Techniques

Microbes in the news