January 31, 2018

Posted on January 31, 2018 by JP Cardenas

Today, research in prediabetes microbiome, bacteriophages in urinary microbiota, several reviews and a good number of papers focused in animal microbiome.

Human Microbiome

Review: Influence of functional food components on gut health – Murphy L.Y. Wan – Critical Reviews in Food Science and Nutrition

Review: Gut Microbiota and the Neuroendocrine System – Aitak Farzi – Neurotherapeutics

Laxative effect of repeated Daiokanzoto is attributable to decrease in aquaporin-3 expression in the colon – Risako Kon – Journal of Natural Medicines

Aberrant intestinal microbiota in individuals with prediabetes – Kristine H. Allin – Diabetologia

Perspective: The Potential for Topical Probiotic Treatment of Chronic Rhinosinusitis, a Personal Perspective – Anders U. Cervin – Frontiers in cellular and infection microbiology

The third tier in treatment: Attending to the growing connection between gut health and emotional well-being – Joseph Verdino – Health psychology open

Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? – Valerio Nobili – Archives of medical science

Kynurenic Acid: The Janus-Faced Role of an Immunomodulatory Tryptophan Metabolite and Its Link to Pathological Conditions – Elisa Wirthgen – Frontiers in immunology

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis – Susana Matamouros – Proceedings of the National Academy of Sciences of the United States of America

Review: Gut as an emerging organ for the treatment of diabetes – Martin Haluzik – The Journal of endocrinology

Bacteriophages Of The Urinary Microbiome – Taylor Miller-Ensminger – Journal of bacteriology

Commensal microbiota modulate gene expression in the skin – Jacquelyn S. Meisel – Microbiome

Host genetic variation and its microbiome interactions within the Human Microbiome Project – Raivo Kolde – Genome medicine

Animal Microbiome

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times – Joung-Soo Lim – Asian-Australasian journal of animal sciences

Effects of different dietary ratio of metabolizable glucose and metabolizable protein on growth performance, rumen fermentation, blood biochemical indices and ruminal microbiota of 8 to 10-month-old heifers – Jie Sun – Asian-Australasian journal of animal sciences

Effects of dietary fiber levels on cecal microbiota composition in geese – Yanpin Li – Asian-Australasian journal of animal sciences

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua – Kiran G. Bapatla – Journal of Basic Microbiology

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model – J.E. Libbey – Beneficial Microbes

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L. – D. Alberoni – Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2 – A. Yitbarek – Beneficial Microbes

Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits – Y. Zhou – Beneficial Microbes

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

Plant/Soil Microbiome

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline – Martin Broberg – Microbiome

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan – Dong Zhu – Environmental science & technology

Environmental Microbiome

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

General Microbiome

Cross-regulatory circuit between AHR and microbiota – Jian Ji – Current Drug Metabolism

‘Massilimalia timonensis’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol – P. Afouda – New microbes and new infections

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies – Stefano Campanaro – Scientific Reports

January 30, 2018

Posted on January 30, 2018 by JP Cardenas

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 28, 2018

Posted on January 28, 2018 by Kiran

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!

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 27, 2018

Posted on January 27, 2018 by Kiran

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

Events and jobs

Adjunct Faculty- Biology, Microbiology, Anatomy & Physiology – St. Louis Community College in Missouri – USA

General microbiome

A Case of Recurrent Pasteurella Bacteremia in an Immunocompetent Patient with No Animal Bite. – F Zarlasht – The American Journal of Case Reports

Pregnancy and early life

Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. – EM Fricke – American Journal of Reproductive Immunology

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants – RD Zwittink – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach – FM Borges – Current Microbiology

Review: Dietary practices and FODMAPs in South Asia: Applicability of the low FODMAP diet to patients with irritable bowel syndrome – SP Hewawasam – Journal of Gastroenterology and Hepatology

Animal experiments

Preprint: Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. – D Fast – bioRxiv

Beneficial effects of Rifaximin in post-infectious irritable bowel syndrome mouse model beyond gut microbiota – Y Jin – Journal of Gastroenterology and Hepatology

Plant, root and soil microbiome

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. – EJ Canter – Ecology

Purple corn-associated rhizobacteria with potential for plant growth promotion – A Castellano-Hinojosa – Journal of Applied Microbiology

Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease – OY de Assis Costa – PLoS One

Biosynthetic and antimicrobial potential of actinobacteria isolated from bulrush rhizospheres habitat in Zhalong Wetland, China – Y Li – Archives of Microbiology

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil – M Pacwa-Płociniczak – Water, Air and Soil Pollution

Water microbiome and extremophile

Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids – H Bestová – Oecologia

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide – A Nishihara – J-Stage

Food microbiology

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing – HNJ Shangpliang – Scientific Reports

Phages and viruses

Preprint: Diversity and evolution of the emerging Pandoraviridae family – M Legendre – bioRxiv

Microbes in the news

Explore the human microbiome in new Delaware natural history museum exhibit – Delaware Public Media

Thoroughness of panel called into question – Delta Optimist

When DNA Went Mobile Some Archaea Jumped Out of the Hot Tub – GEN News

Scientists find 10 new defense systems used by bacteria – Science News

ASTRONAUTS LIVING IN SPACE CAN EAT BACTERIA THAT FEED ON HUMAN WASTE – Newsweek

A Never-Before-Seen Virus Was Just Found in the Sea, and It Kills Bacteria – Inverse Science

Bacteria block transmission of Zika and Dengue viruses – Medical Xpress

First annual thesis competition held at JMU – The Breeze

Microbiome research refines HIV risk for women – EurekAlert

Shimmery bacteria plus a canvas equals art, briefly – Chicago Tribune

BACTERIA THAT HITCH RIDES ON TOOTHBRUSHES, DIAPERS AND OTHER PLASTIC POLLUTION ARE KILLING CORAL REEFS – Newsweek

January 26, 2018

Posted on January 26, 2018 by xinhuang7

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

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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

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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

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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

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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 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 19, 2018

Posted on January 19, 2018 by Anitha Isaiah

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

Posted on January 18, 2018 by TinaS

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?

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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