March 1, 2019

Human Microbiome

The human microbiome in health and disease: hype or hope – Gwen Falony – Acta Clinica Belgica

Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities – Daniel Rodríguez Amor – Life

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome – Ellen Li – PLoS ONE

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites – Kyongbum Lee – Pharmacological Research

Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection – Benjamin H Mullish – Gut

Fecal microbiota dynamics and its relation with disease course in Crohn’s disease – Gianluca Galazzo – Journal of Crohn’s and Colitis

Associations Between Gut Microbiota and Alzheimer’s Disease: Current Evidences and Future Therapeutic and Diagnostic Perspectives – Liang Shen – Journal of Alzheimer’s Disease

Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome – Brooke A. Napier – PNAS

The Human Fecal Microbiota Metabolizes Foodborne Heterocyclic Aromatic Amines by Reuterin Conjugation and Further Transformations – Falco Beer – Molecular Nutrition and Food Research

Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients – Hamzah Abu-Sbeih – Current Gastroenterology Reports

Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease-Focusing on Intestinal Barrier Function – Ida Schoultz – Cells

Can Gut Microbiota and Lifestyle Help Us in the Handling of Anorexia Nervosa Patients? – Vanessa Mendez-Figueroa – Microorganisms

Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases – Maxime Pichon – Healthcare

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria – Allison Dostal Webster – Gut Microbes

Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis – Yan Li – PeerJ

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis – C. Ge – International Journal of Ophthalmology

Gut Microbiota and Chronic Constipation: A Review and Update – Toshifumi Ohkusa – Frontiers in Medicine

An altered fecal microbiota profile in patients with non-alcoholic fatty liver disease (NAFLD) associated with obesity – E. Nistal – The Spanish Journal of Gastroenterology

Paternal Programming of Liver Function and Lipid Profile Induced by a Paternal Pre-Conceptional Unhealthy Diet: Potential Association with Altered Gut Microbiome Composition – X. Zhang – Kidney and Blood Pressure Research

Tryptophan Metabolism and Related Pathways in Psychoneuroimmunology: The Impact of Nutrition and Lifestyle – J. M. Gostner – Neuropsychobiology

The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa – Jochen Seitz – Frontiers in Endocrinology

Sperm Microbiota and Its Impact on Semen Parameters – David Baud – Frontiers in Microbiology

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016 – NIH Human Microbiome Portfolio Analysis Team – Microbiome

 

Microbiome and Cancer

Impact of chemotherapy on the association between fear of cancer recurrence and the gut microbiota in breast cancer survivors – Ryo Okubo – Brain, Behavior, and Immunity

Bugs, drugs, and cancer: can the microbiome be a potential therapeutic target for cancer management? – Biying Chen – Drug Discovery Today

 

Early Childhood Microbiome

Crosstalk Between the Microbiome and Gestational Immunity in Autism-Related Disorders – Matt J. Paysour – DNA and Cell Biology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month – Nina Iszatt – Microbiome

 

Animal Microbiome

Convergence, constraint and the potential for mutualism between ants and gut microbes – Elizabeth G. Pringle – Molecular Ecology

Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy – Martin Schwarzer – Frontiers in Immunology

Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota – Lijuan Sun – Theranostics

 

Beneficial Bugs, Foods and Compounds

Re-purposing is needed for beneficial bugs, not for the drugs – Hari Ram – International Microbiology

Probiotic mixture of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 attenuates hippocampal apoptosis induced by lipopolysaccharide in rats – Ghazaleh Mohammadi – International Microbiology

The Use of Probiotic Therapy to Modulate the Gut Microbiota and Dendritic Cell Responses in Inflammatory Bowel Diseases – Pablo Alagón Fernández del Campo – Medical Sciences

Dietary fibers as emerging nutritional factors against diabetes: focus on the involvement of gut microbiota – Vemana Gowd – Critical Reviews in Biotechnology

Gut microbiota, a new frontier to understand traditional Chinese medicines – Wuwen Feng – Pharmacological Research

Fructooligosaccharides Ameliorating Cognitive Deficits and Neurodegeneration in APP/PS1 Transgenic Mice through Modulating Gut Microbiota – Jing Sun – Journal of Agricultural and Food Chemistry

Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice – Tyler B. Shubitowski – Physiological Reports

Dietary intake of whole strawberry inhibited colonic inflammation in dextran sulfate sodium-treated mice via restoring immune homeostasis and alleviating gut microbiota dysbiosis – Yanhui Han – Journal of Agricultural and Food Chemistry

Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells – Jinli Xie –  Food & Nutrition Research

In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics – Ka-Lung Lam – Molecules

Role of intestinal microecology in the regulation of energy metabolism by dietary polyphenols and their metabolites – Shaoling Lin – Food & Nutrition Research

Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites – Zhi-Lan Zhou – Neurotherapeutics

Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables – Nieves Martínez – Microorganisms

Engineered and wild-type L. lactis promote anti-inflammatory cytokine signalling in inflammatory bowel disease patient’s mucosa – Saša Simčič – World Journal of Microbiology and Biotechnology

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro – Olaf Perdijk – Frontiers in Immunology

 

Built Environments

Man-made microbial resistances in built environments – Alexander Mahnert – Nature Communications

House dust microbiome and human health risks – Yifan Shan – International Microbiology

Microbiomes of China’s Space Station During Assembly, Integration, and Test Operations – Ying Zhang – Microbial Ecology

 

Environmental and Plant Microbiome

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses – Cesar A. Pérez-Fernández – International Microbiology

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils – Zhi-Bo Zhao – Microbiome

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

 

Bioinformatics

Batch effects correction for microbiome data with Dirichlet-multinomial regression – Zhenwei Dai – Bioinformatics

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cuscó – F1000Research

 

Methods

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis – Xiaoxiao Sun – PeerJ

In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media – Marie Wahlgren – Pharmaceutics

 

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February 13, 2019

Today’s digest features a study on leaf-associated microbiomes of grafted tomato plants, study that reveals the chemical “fingerprint” and contribution of Parasutterella to host health, and Everything Hertz podcast with episode “Promiscuous expertise”. Happy reading/listening!

Gut microbiome

A new genomic blueprint of the human gut microbiota – Alexandre Almeida – Nature

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana – Matthew E. B. Hansen – Genome Biology

Disturbance of trace element and gut microbiota profiles as indicators of autism spectrum disorder: A pilot study of Chinese children – Qixiao Zhai – Environmental Research

*Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota – Tingting Ju – The ISME Journal

Extensive transmission of microbes along the gastrointestinal tract – Thomas Sebastian Benedikt Schmidt – eLife

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz – bioRxiv

Skin microbiome

Review: Microbiosis in pathogenesis and intervention of atopic dermatitis – Jianhua Dou – International Immunopharmacology

Plant/root/soil microbiome

*Leaf-associated microbiomes of grafted tomato plants – Hirokazu Toju – Scientific Reports

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment – Jarosław Grządziel and Anna Gałązka – Frontiers in Microbiology

Podcast

*Episode 77: Promiscuous expertise – Dan Quintana and James Heathers – Everything Hertz [A great episode about scientists who claim to be a public authority on topics outside their area of expertise!]

February 1, 2019

Today’s digest is quite diverse: the respiratory microbiome networks in cystic fibrosis patients, ketogenic diet effects on the gut microbiota in children with severe epilepsy, and insect-associated Streptomyces (spoiler: inhibit antimicrobial-resistant pathogens more than soil Streptomyces). Happy reading!

General microbiome

Minireview: The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases – A H Bishop – FEMS Microbiology Letters

Transforming medicine with the microbiome – Niv Zmora – Science Translational Medicine

Gut microbiome

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease – Shun He – Nature

*The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy – Marie Lindefeldt – npj Biofilms and Microbiomes

Vaginal microbiome

Association between vaginal washing and vaginal bacterial concentrations – Michelle C. Sabo – PlosOne

Skin microbiome

Investigation of the Skin Microbiome: Swabs vs Biopsies – S. Prast‐Nielsen – British Journal of Dermatology

Oral microbiome

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents – A. Esberg – Scientific Reports

Respiratory microbiome

*Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations – Mehdi Layeghifard – npj Biofilms and Microbiomes

Plant/root/soil microbiome

Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure – Zhen Guo – PlosOne

Water microbiome

Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region – Andrew Camero – PlosOne

Animal experiments

Cream Cheese-Derived Lactococcus chungangensis CAU 28 Modulates the Gut Microbiota and Alleviates Atopic Dermatitis in BALB/c Mice – Jong-Hwa Kim – Scientific Reports

Animal Microbiome

*The antimicrobial potential of Streptomyces from insect microbiomes – Marc G. Chevrette – Nature Communications

January 28, 2019

Human and General Microbiome

Book Chapter: Necrotizing Enterocolitis and the Preterm Infant Microbiome. – Jillian R. Baranowski – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Shaping Microbiota During the First 1000 Days of Life. – Marta Selma-Royo – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Targeting Food Allergy with Probiotics. – Lorella Paparo – Part of the Advances in Experimental Medicine and Biology book series

Review: The relation of the vaginal microbiota to early pregnancy development during In Vitro Fertilization treatment-A meta-analysis. – M. Singer – Journal of Gynecology Obstetrics and Human Reproduction

Review: Neuropeptides in the microbiota-brain axis and feeding behavior in autism spectrum disorder. – Sergueï O.Fetissov – Nutrition (Elsevier)

Review: Gut microbiome and cancer immunotherapy. – Weina Li – Cancer Letters

Review: The Microbiome-Host Interaction as a Potential Driver of Anastomotic Leak. – Victoria M. Gershuni – Current Gastroenterology Reports

Review: The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD). – Zahra Safari – Cellular and Molecular Life Sciences

Review: The role of chronic kidney disease-associated dysbiosis in cardiovascular disease.  – Mark A Bryniarski – Experimental Biology and Medicine

Review: The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer. – Rossella Cianci – International Journal of Molecular Sciences

Spotlight: Ethnicity-Influenced Microbiota: A Future Healthcare Perspective. – Madhusmita Dehingia – Trends in Microbiology

Exploration of microbiota targets for major depressive disorder and mood related traits. – Yu-Chu Ella Chung – Journal of Psychiatric Research

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. – Farnaz Heidarian – Current Research in Translational Medicine

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways. – Katarzyna Pienkowska – Journal of Cystic Fibrosis

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. – Jay Liu – EBioMedicine

Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects. – Eri Ikeda – Clinical Oral Investigations

Close social relationships correlate with human gut microbiota composition. – Kimberly A. Dill-McFarland – Scientific Reports

The gut microbiota heterogeneity and assembly changes associated with the IBD. – Yang Sun – Scientific Reports

The respiratory microbiota: new insights into pulmonary tuberculosis. – Setegn Eshetie – BMC Infectious Diseases

 

Faecal Transplants

Letter to the Editor: Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish – Clinical Microbiology and Infection

Clinical characteristic and fecal microbiota responses to probiotic or antidepressant in patients with diarrhea-predominant irritable bowel syndrome with depression comorbidity: a pilot study. – Lu Zhang – Chinese Medical Journal

Multi-session fecal microbiota transplantation using colonoscopy has favorable outcomes for the treatment of steroid-dependent ulcerative colitis. – Young-Seok Cho – Intestinal Research

 

Beneficial Microbes and Compounds

Effect of Probiotic Use on Adverse Events in Adult Patients with Inflammatory Bowel Disease: a Retrospective Cohort Study. – Maria Pina Dore – Probiotics and Antimicrobial Proteins

Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells. – Ludovica Marinelli – Scientific Reports

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2′-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. – Manuela Centanni – Applied and Environmental Microbiology

Oral supplements of combined fructo- and xylo-oligosaccharides during perinatal period significantly offsets acrylamide-induced oxidative impairments and neurotoxicity in rats. – Muralidhara Krishna – Journal Of Physiology And Pharmacology

Impact of Grain Sorghum Polyphenols on Microbiota of Normal Weight and Overweight/Obese Subjects during In Vitro Fecal Fermentation. – Danielle Ashley – Nutrients

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China. – Mengfan Ding – Food & Function

 

Animal Microbiome

Review: The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. – Sarah Moraïs – Trends in Microbiology

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster. – Huili Qiao – Journal of Experimental Biology

Genomic diversity landscape of the honey bee gut microbiota. – Kirsten M. Ellegaard – Nature Communications

Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. – Jie Zhang – Neuroscience and Therapeutics

Functional Interactions between Gut Microbiota Transplantation, Quercetin and High Fat Diet Determine Non-Alcoholic Fatty Liver Disease Development in Germ-Free Mice. – David Porras – Molecular Nutrition and Food Research

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. – Giulia Alessandri – Environmental Microbiology

 

Environmental Microbiome

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams. – Silas H.W.Vick – iScience

 

Food Microbiome

Book Chapter: Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health. – Laura Lavefve – Advances in Food and Nutrition Research

 

Methodologies

Review: A crash course in sequencing for a microbiologist. – Aleksandra Kozińska – Journal of Applied Genetics

Review: The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. – Pavan K. Mantravadi – Antibiotics

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. – Julien Tap – Scientific Reports

A sensitive GC/MS detection method for analyzing microbial metabolites short chain fatty acids in fecal and serum samples. – Shuming Zhang – Talanta

January 25, 2019

General microbiome

A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – Chao Zhang – Frontiers in Microbiology

Review: Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment – Muneer Ahmad Malla – Frontiers in Immunology

The microbiome and its relevance in complex wounds – Francesco Drago – European Journal of Dermatology

Commentary: A Link between the Gut and Bone: Bone Health Impacted by Changes in Gut Microbiota – Larry J.Suva – The American Journal of Pathology

Pregnancy and early life

Feeding intolerance alters the gut microbiota of preterm infants – Zhenya Yuan – PLOS ONE

Multi-site human microbiome

Review: A correlation between intestinal microbiota dysbiosis and osteoarthritis – Marta AnnaSzychlinska – Heliyon

Human respiratory microbiome

A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy – Giovanna Elisiana Carpagnano – BMC Infectious Diseases

The Association Between Disease Severity and Microbiome in Chronic Rhinosinusitis – Darren Rom – The Laryngoscope

Review: Microbiota and asthma: Clinical implications – Konstantinos Katsoulis – Respiratory Medicine

Human oral microbiology

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Periodontal pathogens are a risk factor of oral cavity squamous cell carcinoma, independent of tobacco and alcohol and human papillomavirus – Ian Ganly – International Journal of Cancer

Human gut microbiome

Review: Role of diet and gut microbiota on colorectal cancer immunomodulation – Carolina Vieira De Almeida – World Journal of Gastroenterology

Review: Targeting obesity management through gut microbiota modulation by herbal products: A systematic review – Hanieh-SadatEjtahed – Complementary Therapies in Medicine

Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility – Vasudevan Dinakaran – Frontiers in Microbiology

Animal experiments

Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves – Raies A. Mir – PLOS ONE

Advanced Age Impairs Intestinal Antimicrobial Peptide Response and Worsens Fecal Microbiome Dysbiosis Following Burn Injury in Mice – Elizabeth G Wheatley – Shock

Effects of drought‐stressed temperate forage legumes on the degradation and the rumen microbial community in vitro – Susanne Riede – Journal of Animal Physiology and Animal Nutrition

Bacillus amyloliquefaciens ameliorates Dextran Sulfate Sodium-Induced Colitis by Improving Gut Microbial Dysbiosis in Mice Model – Guangtian Cao – Frontiers in Microbiology

Bacillus subtilis 29784 induces a shift in broiler gut microbiome toward butyrate-producing bacteria and improves intestinal histomorphology and animal performance – Vincent Jacquier – Poultry Science

Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐abundance Groups Correlating with the Blood Glucose Lowering Effect – Tingting Chen – Molecular Nutrition and Food Research

Influence of Porphyromonas gingivalis in gut microbiota of streptozotocin‐induced diabetic mice – Anri Ohtsu – Oral diseases

Plant, root, and soil microbiome

Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues – Aline Bronzato Badial – Plant Disease

Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection – Dongmei Zhou – Microbial Ecology

Water and extremophile microbiome

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations – Natàlia Corcoll – Frontiers in Microbiology

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity – Nicola Vitulo – Frontiers in Microbiology

Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation – Jian-liLiu – Environmental Pollution

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge – Jie Gao – Journal of Environmental Sciences

Food microbiology

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization – Javier Alonso‐del‐Real – Environmental Microbiology

Phages and viruses

Commentary : Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer – Scott A. Handley – mBio

January 23, 2019

Today’s digest is about the distinct microbial networks within disturbed gut microbiome, multifaceted roles of Staphylococcus epidermidis in skin physiology, and high-throughput cultivation techniques. Happy reading!

Urinary microbiome

Review: The Microbiome and Genitourinary Cancer: A Collaborative Review – Mark C. Markowski – European Urology

Gut microbiome

*Microbial network disturbances in relapsing refractory Crohn’s disease – Bahtiyar Yilmaz – Nature Medicine

Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma – Qisha Liu – Gut Pathogens

Human gut microbes are susceptible to antimicrobial food additives in vitro – Lucia Hrncirova – Folia Microbiologica

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health – Nilusha Malmuthuge – Applied and Environmental Microbiology

Skin microbiome

*Microbial guardians of skin health – Apollo Stacy and Yasmine Belkaid – Science

Water microbiome

Comparison of microbial communities in the sediments and water columns of frozen cryoconite holes in the McMurdo Dry Valleys, Antarctica – Pacifica Sommers – Frontiers in Microbiology

Plant/root/soil microbiome

Invasive plant species identity affects soil microbial communities in a mesocosm experiment – Anna M. Stefanowicz – Applied Soil Ecology

Techniques

*High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria – Dennis Versluis – PlosOne

*Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium – Viola Kurm – PlosOne

January 22, 2019

Today’s digest is packed with interesting reviews from Gut to Rhizosphere microbiomes.

General Microbiome

Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.Heras VL. Microbiome.

Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri. Oh JH. Cell Host snd Microbe.

Gut Microbiome

REVIEW: The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?Knox NC. Current Treatment Options in Gastroenterology

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites.Ding Y. Pharmacological Research

Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease.van Kessel SP. Nature Communications

Lung Microbiome

Multiple respiratory microbiota profiles are associated with lower airway inflammation in children with protracted bacterial bronchitis. Marsh RL. Chest.

Plant, Soil, and Air Microbiome

Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth. Jiao S. Applied Environmental Microbiology

Effect of plant growth promoting bacterium; Pseudomonas putida UW4 inoculation on phytoremediation efficacy of monoculture and mixed culture of selected plant species for PAH and lead spiked soils.Afegbua SL. International Journal of Phytoremediation.

REVIEW: Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils.Asemoloye MD. International Journal of Phytoremediation

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars.Materatski P. Fungal Biology

Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton.Wei Z. Fungal Biology.

REVIEW: To Fix or Not To Fix: Controls on Free-Living Nitrogen-Fixation in the Rhizosphere.Smercina DN. Applied Environmental Microbiology

An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species.Bucher T. Environmental Microbiology

Diversity analysis of the rhizospheric and endophytic bacterial communities of <i>Senecio vulgaris</i> L. (Asteraceae) in an invasive range. Cheng D. PeerJ

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.Zhong Y. Plant, Cell, and Environment

Animal Experiments and Microbiome

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.Keijser BJF. BMC Genomics

Earthworms and cadmium – Heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?  Šrut M. Ecotoxicology and Environmental

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health. Malmuthuge N. Applied Environmental Microbiology

Inland Waters and Marine Microbiomes

High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.Plotnikov AO. Microbial Ecology

Action of oxytetracycline (OTC) degrading bacterium and its application in Moving Bed Biofilm Reactor (MBBR) for aquaculture wastewater pre-treatment.Shao S. Ecotoxicology and Environmental

Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports. Gerhard WA. Environment International