Category Archives: Microbial Ecology

January 28, 2019

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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

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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

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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

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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

January 15, 2019

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Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv

January 14, 2019

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Human/General Microbiome

Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes – Richard G. Brown – Translational Research

Sex differences in the gut microbiota as potential determinants of gender predisposition to disease – Jose A. Santos‐Marcos – Molecular Nutrition and Food Research

AllergoOncology: microbiota in allergy and cancer – an EAACI position paper – E Untersmayr – Allergy

Comment: Gut microbiota and hypertension – Jun-ichi Oyama – Hypertension Research

Comment: Host-microbiota interactions: from holobiont theory to analysis – Jean-Christophe Simon – Microbiome

Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients – Luma Al-Bayati – Archives of Iranian Medicine

What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases – Emanuele Rinninella – Microorganisms

A Prospective Study In Severely Injured Patients Reveals An Altered Gut Microbiome Is Associated With Transfusion Volume – Susannah E. Nicholson – Journal of Trauma and Acute Care Surgery

Review: Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms – Tsuyoshi Hamada – The Journal of Pathology

Review: Targeting gut microbiota with dietary components on cancer: Effects and potential mechanisms of action – Jun Tao – Critical Reviews in Food Science and Nutrition

Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study – Li Shao – Frontiers in Microbiology

Review: Leveraging Multilayered “Omics” Data for Atopic Dermatitis: A Road Map to Precision Medicine – Debajyoti Ghosh – Frontiers in Immunology

Systemic instruction of cell-mediated immunity by the intestinal microbiome – John Grainger – F1000Research

Fecal microbiota transplantation in refractory ulcerative colitis – a case report – B. D. Moutinho – Journal of International Medical Research

Current Opinion: Acne, the Skin Microbiome, and Antibiotic Treatment – Haoxiang Xu – American Journal of Clinical Dermatology

Fusobacterium nucleatum promotes chemoresistance to 5-fluorouracil by upregulation of BIRC3 expression in colorectal cancer – Sheng Zhang – Journal of Experimental & Clinical Cancer Research

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

 

Animal Models

Obesity Aggravates Acute Pancreatitis via Damaging Intestinal Mucosal Barrier and Changing Microbiota Composition in Rats – Cheng Ye – Scientific Reports

Asperlin Stimulates Energy Expenditure and Modulates Gut Microbiota in HFD-Fed Mice – Chongming Wu – Marine Drugs

Preventive Effect of Spontaneous Physical Activity on the Gut-Adipose Tissue in a Mouse Model That Mimics Crohn’s Disease Susceptibility – Florie Maillard – Cells

Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo‐Min Jang – Molecular Nutrition and Food Research

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome – Heidi H. Pak – Scientific Reports

 

More Animal Microbiomes

Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory – Jewelna Akorli – Parasites & Vectors

Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita – Nancy Weiland-Bräuer – Scientific Reports

 

Beneficial Microbes and Compounds

Review: Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health – Francisco A. Tomás-Barberán – Annual Reviews of Food Science and Technology

Dietary Fructooligosaccharide and Glucomannan Alter Gut Microbiota and Improve Bone Metabolism in Senescence-Accelerated Mouse – Kenichi Tanabe – Journal of Agricultural and Food Chemistry

 

Plant Microbiome

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome – Joy Bergelson – Scientific Reports

 

January 11, 2019

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General Microbiome

A great-ape view of the gut microbiome.Nishida AH. Nature Reviews Genetics

Relative reduction of biological and phylogenetic diversity of the oral microbiota of diabetes and pre-diabetes patients. Saeb ATM. Microbial Pathogenesis

Dietary modulation of the microbiome as therapy.Bernard NJ. Nature Reviews Rheumatology

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.Pacheco AR. Nature Communications

Low-moisture food matrices as probiotic carriers. Marcial-Coba MS . FEMS Microbiology Letters

REVIEW: Cross-Domain and Viral Interactions in the Microbiome.Rowan-Nash AD. Microbiology and Molecular Biology Reviews

The respiratory microbiome and susceptibility to influenza virus infection. Lee KH. PLoS One

Food Microbiome

Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.Marino M. Food Microbiology

Gut Microbiome

Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.Singh R. Nature Communications

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.Sanctuary MR. PLoS One

Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate <i>Clostridium difficile</i> Colitis while Dysregulating the Inflammatory Response.Maseda D. mBio

Techniques/Resources

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes. Yadav D. DNA Research

Streamlining standard bacteriophage methods for higher throughput.Kauffman KM. MethodsX

Indirect DNA extraction method suitable for acidic soil with high clay content. Högfors-Rönnholm E. MethodsX

DATABASE: The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection.Rigden DJ. Nucleic Acid Research

Animal Experiments and Microbiome

Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.Treichel NS. Microbial Ecology

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.Miranda-CasoLuengo R. PLoS One.

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.Ramírez-Fernández L. PLoS One

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota.Kollarcikova M. Poultry Science

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.Delgado B. Scientific  Reports

 

Marine and Inland Waters

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.de Sousa AGG. Microbial Ecology

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure.Loick-Wilde N. Global Change Biology

Analysis of viral and bacterial communities in groundwater associated with contaminated land.Costeira R. Science of the Total Environment

Plant, Soil, and Air Microbiome

The known and the unknown in soil microbial ecology. Baldrian P. FEMS Microbiology Ecology.

Genomic analysis of bacteria in the Acute Oak Decline pathobiome.Doonan J. Microbial Genomics.

Glutathione S-Transferase Enzymes in Plant-Pathogen Interactions.Gullner G. Frontiers in Plant Science

A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.  Cota-Ruiz K. Environmental International

Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California. Ottesen A. Food Microbiology

Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application.Rieke EL. Frontiers of Microbiology

January 7, 2019

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Happy Monday! Today’s digest includes the influence of ant colonies on soil microbes, the assembly of prokaryotic communities in subtropical grasslands, and lactic acid bacteria isolated from sourdough. Have a great week!

Human gut microbiome

Review: The gut microbiome in anorexia nervosa: relevance for nutritional rehabilitation – Ruusunen – Psychopharmacology

Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children – Zhong – Microbiome

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases – Armstrong – Microbiome

Animal experiments

Preprint: The gut microbiota is associated with clearance of Clostridium difficile infection independent of adaptive immunity – Leslie – BioRxiv

Animal microbiome

Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves – Murphy – Microbial Ecology

Modulation of broiler gut microbiota and gene expression of Toll-like receptors and tight junction proteins by diet type and inclusion of phytogenics – Paraskeuas – Poultry Science

Plant, root, and soil microbiome

Responses of soil aggregates and bacterial communities to soil-Pb immobilization induced by biofertilizer – Wang -Chemosphere

Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland – Lupatini – Microbial Ecology

Ant colonies promote the diversity of soil microbial communities – Delgado-Baquerizo – ISME

Water and extemophile microbiome

Morphological response to salinity, temperature, and pH changes by marine fungus Epicoccum nigrum – Ahumada-Rudolph – Environmental Monitoring and Assessment

Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica – Arce-Rodríguez – Extremophiles

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera – Yang – Microbiome

Water pollution and observation of acquired antibiotic resistance in Bayou Lafourche, a major drinking water source in Southeast Louisiana, USA – Bird – Environmental Science and Pollution Research

Metagenomic Analysis of Zinc Surface–Associated Marine Biofilms – Ding – Microbial Ecology

Evolutionary constraints on species diversity in marine bacterioplankton communities – Lu – ISME

Built environment

Wastewater treatment and microbial community dynamics in a sequencing batch reactor operating under photosynthetic aeration – Parakh – Chemosphere

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics – Zhu – Water Research

Food microbiology

Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota – Pérez-Burillo – Food Chemistry

In vitro and in vivo investigations of probiotic properties of lactic acid bacteria isolated from Chinese traditional sourdough – Li – Applied Microbiology and Biotechnology

Bacterial community dynamics and physical–chemical characteristics in natural fermentation of jiang‐shui, a traditional food made in Northwest China – Liu – Science of Food and Agriculture

Science, publishing, and career

Here’s what scientists searched for in 2018: AI is up, stress is down – Kelly Oakes – Nature News

January 4, 2019

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Highlights of today’s Digest include: animal microbiomes from snakes to bald eagles to porcupines, studies of bacteria promoting plant growth, and a nice review of ‘omics in fermented foods. Happy reading!

Human oral microbiome
Microcosm biofilms cultured from different oral niches in periodontitis patients – Fabian Cieplik – Journal of Oral Microbiology

Xylitol and sorbitol effects on the microbiome of saliva and plaque – Reisha Rafeek – Journal of Oral Microbiology

Human vaginal microbiome
Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis – Hui-Mei Chen – BMC Genomics

Human gut microbiome
Five years of fecal microbiota transplantation – an update of the Israeli experience – Sharon A Greenberg – World Journal of Gastroenterology

Review: Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: A systematic review – Petra Zimmermann – Journal of Allergy and Clinical Immunology

Interplay between food and gut microbiota in health and disease – Niels Banhos Danneskiold-Samsøe – Food Research International

Gut microbiome changes in overweight male adults following bowel preparation – Hui-Mei Chen – BMC Genomics

Animal Microbiome
Preprint: Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A. – Rocio Crespo – bioRxiv

Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India – Sajesh Puthenpurackal Krishnankutty – Journal of Venomous Animals and Toxins including Tropical Diseases

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei – Yang Du – Fish & Shellfish Immunology

Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics – Mackenzie Thornbury – PLOS One

Plant, root, and soil microbiome
Review: Planting the Microbiome – Jennifer K. Spinler – Trends in Microbiology

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins – Johannes Thürich – PLOS One

Screening of plant growth promotion ability among bacteria isolated from field-grown sorghum under different managements in Brazilian drylands – Jéssica Fernanda da Silva – World Journal of Microbiology and Biotechnology

Streptomyces: implications and interactions in plant growth promotion – Oluwaseyi Samuel Olanrewaju – Applied Microbiology and Biotechnology

Mycorrhizal features and leaf traits covary at the community level during primary succession – J. Rasmus P. Jespersen – Fungal Ecology

Microbial communities controlling methane and nutrient cycling in leach field soils – Cristina P.Fernandez-Baca – Water Research

Gradients of three coastal environments off the South China Sea and their impacts on the dynamics of heterotrophic microbial communities – Xianhua Liu – Science of the Total Environment

New insights into the impact of nZVI on soil microbial biodiversity and functionality – Carmen Fajardo – Journal of Environmental Science and Health, Part A

Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite – Melissa K.Corbett – Research in Microbiology

Removal of veterinary antibiotics in constructed wetland microcosms – Response of bacterial communities – Filipa Santos – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics – Francesco Danza – PLOS One

Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin – Guoke Chen – Bioresource Technology

Food Microbiology
Omics in traditional vegetable fermented foods and beverages – Jocelin Rizo – Critical Reviews in Food Science and Nutrition

Preprint: Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation – Qun Wu – bioRxiv

Bioinformatics
A latent allocation model for the analysis of microbial composition and disease – Ko Abe – BMC Bioinformatics

Techniques
Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome – Matthew J. Scarborough – mSystems

December 30, 2018

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In the midst of the festive season have a fiesta with the recent articles on Microbiome. Todays MicroBiome Digest covers the Techniques and Treatments, Drugs, Immunostimulatory Diet and Nutrition, Multivariate Count Data Model, Antimicrobials, Pre/Pro-biotcs, Host-Microbe Interactions, Genes, Genomics and Pathways of Microbiota, Infant Microbiome, Animal Models, Animal Microbiome, Microbial Ecology of plant and soil. Happy Reading!!! 

TECHNIQUES & TREATMENTS:

LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation – Mathieu Seppey – bioRxiv

Single-cell virus sequencing of influenza infections that trigger innate immunity – Alistair B Russell – bioRxiv

METHODS TO IMPROVE INDUCTION OF IGG AND IGA ANTIBODIES BY VACCINES – Boyaka, Prosper -United States Patent Application 20180360953 -PATENT

Are the Statins promising antifungal agents against invasive candidiasis? – William GustavoLima -Biomedicine & Pharmacotherapy

Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data – Lee KH – Biostatistics

Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing – Mu DS – Microbiome

Prognostic Impact of Fusobacterium nucleatum Depends on Combined Tumor Location and Microsatellite Instability Status in Stage II/III Colorectal Cancers Treated with Adjuvant Chemotherapy – Oh HJ – J Pathol Transl Med.

Loss of Gut Microbiota Alters Immune System Composition and Cripples Post-Infarction Cardiac Repair – Tang TW – Circulation

DRUG, DIET and NUTRITION:

Review article: implementation of a diet low in FODMAPs for patients with irritable bowel syndrome-directions for future research – Mitchell Hrticle – Aliment Pharmacol Ther.

Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function – Cai Y – J Gastroenterol Hepatol.

Rifaximin Altered Gut Microbiota Components Associated with Liver/Neuropsychological Functions in Patients with Hepatic Encephalopathy: An Exploratory Data Analysis of a Phase II/III Clinical Trials – Kawaguchi T – Hepatol Res.

Inulin ameliorates alcoholic liver disease via suppressing LPS-TLR4-Mψ axis and modulating gut microbiota in mice – Yang X – Alcohol Clin Exp Res.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease – Yoshida N – J Atheroscler Thromb.

Late gestation diet supplementation of resin acid-enriched composition increases sow colostrum immunoglobulin G content, piglet colostrum intake and improve sow gut microbiota – Hasan S – Animal

PRE/PRO- BIOTICS and ANTIMICROBIAL:

The human skin microbiota is a rich source of bacteriocin producing staphylococci which kill human pathogens – O’Sullivan JN – FEMS Microbiol Ecol.

Comparative immunostimulatory effect of probiotics and prebiotics in Channa punctatus against Aphanomyces invadans – Devi G – Fish Shellfish Immunol

GENES, GENOMICS & PATHWAYS:

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients – Yousif Mohammed Alfatih – bioRxiv

Review: Interactions Between Autophagy and the Unfolded Protein Response: Implications for Inflammatory Bowel Disease – Hooper KM – Inflamm Bowel Dis.

In vitro and in vivo characterization of Clostridium scindens bile acid transformations – Marion S- Gut Microbes

Bioinformatic, phylogenetic, and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia – D’Agostino PM – Environ Microbiol

Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses – Tyakht AV – BMC Genomics

Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan – Sekizuka T – mSphere

HOST-MICROBE INTERACTION:

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P Pagé -bioRxiv

Bacterial secretion of histamine within the gut influences immune responses within the lung – Barcik W – Allergy

GUT MICROBIOME:

Extensive Transmission of Microbes along the Gastrointestinal Tract – Thomas SB Schmidt – bioRxiv

VAGINAL MICROBIOME:

Human β-defensin-2 as a biochemical indicator of vaginal environment in pregnant women – Hideko Kotani – Hypertension Research In Pregnancy

PREGNANCY AND EARLY LIFE:

Physiology of Stress and Use of Skin-to-Skin Care as a Stress-Reducing Intervention in the NICU – Britt Frisk Pados – Nursing for Women’s Health

Longitudinal analysis of infant stool bacteria communities before and after acute febrile malaria and artemether/lumefantrine treatment – Mandal RK – J Infect Dis.

Haemophilus-dominant nasopharyngeal microbiota is associated with delayed clearance of respiratory syncytial virus in infants hospitalized for bronchiolitis – Mansbach JM – J Infect Dis

ANIMAL MODEL EXPERIMENTS:

Dietary nucleotides can directly stimulate the immunity of zebrafish independent of the intestinal microbiota – Guo X – Fish Shellfish Immunol.

Antimicrobial assessment of phage therapy using a porcine model of biofilm infection – Milho C – Int J Pharm

ANIMAL MICROBIOME:

Effect of different levels of tryptophan on productive performance, egg quality, blood biochemistry, and caecal microbiota of hens housed in enriched colony cages under commercial stocking density – Khattak F -Poult Sci.

Exogenous carbohydrases added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs – Li Q – J Anim Sci.

Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment – Berlanga M – PLoS One

MICROBIAL ECOLOGY:

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia – Yasir M – OMICS

Rhizosphere microorganisms can influence the timing of plant flowering – Lut T – Microbiome