November 27, 2018

Microbial communities of IBS patients after fecal microbiota transplantation, the shipworm gill-associated microbiota, a profile of bioartist Ani Liu in our “bacteria art” section.

Human skin microbiome

The Microbiome in Atopic Dermatitis – Amy S Paller – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Microbiome dynamics in obesity – Christoph A Thaiss – Science

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation – Tarek Mazzawi – PLOS ONE

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential – Christopher Bulow – mSphere

Comparison of the gut microbiota of obese individuals from different geographic origins – Emmanouil Angelakis – New Microbes and New Infections

Review: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome – Manosha Perera – International Journal of Medical Reviews

Animal experiments

Proteomic Analysis of Microbial Induced Redox-Dependent Intestinal Signaling – Jason D Matthews – Redox Biology

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites – Jan Hubert – Microbial Ecology

Animal microbiome

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans – Francesca Scolari – BMC Microbiology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Thais L Brito – PLOS ONE

Plant, root, and soil microbiome

Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita – Refik Bozbuga – Scientific Reports

The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil – F Bastida – Geoderma

Review: Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review – Tong Yu – Science of the Total Environment

Water and extremophile microbiome

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics – Mary K Donovan – Scientific Reports

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China – Shilei Sang – Scientific Reports

Bioinformatics

Pre-print: Naught all zeros in sequence count data are the same – Justin D Silverman – bioRxiv

Microbes in the news

A bacterium’s enemy isn’t your friend – Michael S. Gilmore – Nature

Bacteria art

Portrait of the Artist as a Microbial Growth – Kevin Litman-Navarro – The Outline

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November 10, 2018

Human and General Microbiome

Review: Clinical Application and Potential of Fecal Microbiota Transplantation – R.E. Ooijevaar – Annual Review of Medicine

Editorial: A novel treatment for patients with constipation: Dawn of a new age for translational microbiome research? – Ayesha Shah – Indian Journal of Gastroenterology

Research Highlight: Of ethnicity, environment, and microbiota – Sundararajan Jayaraman – Cellular & Molecular Immunology

Minireview: Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder – Rachael Horne – Frontiers in Psychiatry

Case Report: Hirschsprung’s Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome – Georg Singer – Case Reports in Pediatrics

News and Views: Rules of engagement in the gut microbiome – Elze Rackaityte – Nature Medicine

Preview: When Soluble Fibers Meet Hepatocellular Carcinoma: The Dark Side of Fermentation – Suchira Gallage – Cell Metabolism

Preview: A Microbiota Assimilation – Justin Sonnenburg – Cell Metabolism

Fecal microbiota transplantation: restoring the injured microbiome after allogeneic hematopoietic cell transplantation – Zachariah DeFilipp – Biology of Blood and Marrow Transplantation

Studies of nonhuman primates: key sources of data on zoonoses and microbiota – B.Davoust – New Microbes and New Infections

Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition –  Cristian Pasquaretta – Genes

Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans – Jennifer R. Bratburd – mBio

A randomized double-blind placebo-controlled trial showing rifaximin to improve constipation by reducing methane production and accelerating colon transit: A pilot study – Uday C. Ghoshal – Indian Journal of Gastroenterology

Zinc Deficiency and the Recurrence of Clostridium difficile Infection after Fecal Microbiota Transplant: A Retrospective Cohort Study – Blake A. Niccum – Journal of Nutrition and Metabolism

Recurrent Clostridium difficile Infection: Risk Factors, Treatment, and Prevention – Jung Hoon Song – Gut and Liver

Profiles and Perspectives: Mitochondrial dysfunction and gut microbiota imbalance: An intriguing relationship in chronic kidney disease – Denise Mafra – Mitochondrion

Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population – Filipa Godoy-Vitorino – Frontiers in Microbiology

Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels – Mary Rodríguez-Rabassa – International Journal of Environmental Research and Public Health

Minireview: Human bacterial repertoire of the urinary tract: a potential paradigm shift – Aurélie Morand – Journal of Clinical Microbiology

Review: Role of gut microbiota in intestinal wound healing and barrier function – Ashfaqul Alam – Tissue Barriers

Initial microbial community of the neonatal stomach immediately after birth – Sarah Bajorek – Gut Microbes

The Role of Diet, Micronutrients and the Gut Microbiota in Age-Related Macular Degeneration: New Perspectives from the Gut⁻Retina Axis – Emanuele Rinninella – Nutrients

Review: Candida Interactions with the Oral Bacterial Microbiota – Daniel Montelongo-Jauregui – Journal of Fungi

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants – Elena Biagi – Frontiers in Microbiology

First Insights into the Gut Microbiota of Mexican Patients with Celiac Disease and Non-Celiac Gluten Sensitivity – Jose F. Garcia-Mazcorro – Nutrients

Dietary Exposure to the Environmental Chemical, PFOS on the Diversity of Gut Microbiota, Associated With the Development of Metabolic Syndrome – Keng Po Lai – Frontiers in Microbiology

 

Death Microbiome

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue – Whitney A. Kodama – Journal of Forensic Sciences

 

Animal Microbiome / Animal Experiments

Review: Chicken Gut Microbiota: Importance and Detection Technology –  Yue Shang – Frontiers in Veterinary Sciences

Predator odor exposure in early adolescence influences the effects of the bacterial product, propionic acid, on anxiety, sensorimotor gating, and acoustic startle response in male rats in later adolescence and adulthood – Deanne Tak On Wah – Physiology & Behavior

Pharmacological Activation of PXR and CAR Down-regulates Distinct Bile Acid-metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis – Joseph L Dempsey – Toxicological Sciences

Protective effects of ghrelin on fasting-induced muscle atrophy in aging mice – Chia-Shan Wu – The Journals of Gerontology: Series A

The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice – Bei Gao – Chemical Research in Toxicology

Differential effects of coconut versus soy oil on gut microbiota composition and predicted metabolic function in adult mice – Vania Patrone – BMC Genomics

Pharmaceutical Impact of Houttuynia Cordata and Metformin Combination on High-Fat-Diet-Induced Metabolic Disorders: Link to Intestinal Microbiota and Metabolic Endotoxemia – Jing-Hua Wang – Frontiers in Endocrinology

Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice – Umesh D. Wankhade – Scientific Reports

Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice – Naoki Sasaki –  Frontiers in Microbiology

Effect of Grifola frondosa 95% ethanol extract on lipid metabolism and gut microbiota composition in high-fat diet-fed rats – Yu-Yang Pan – Food & Function

Reduction in butyrate-producing Lachnospiraceae contributes to stress-induced visceral hypersensitivity in rats – Jindong Zhang – Journal of Gastroenterology and Hepatology

 

Beneficial Compounds and Probiotics

Review: Potential Prebiotic Properties of Nuts and Edible Seeds and Their Relationship to Obesity – Clara S. A. Sugizaki – Nutrients

Review: Resveratrol, Metabolic Syndrome, and Gut Microbiota – Alice Chaplin – Nutrients

Isolation and Characterization of Potentially Probiotic Bacterial Strains from Mice: Proof of Concept for Personalized Probiotics – Larissa S. Celiberto – Nutrients

Two alkaline motifs in the Lactobacillus salivarius Lv72 OppA surface are important to its adhesin function – C. Martín – Beneficial Microbes

 

Protocols

Book Chapter: Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology

 

Bioinformatics

Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome – Huiru Zheng – IEEE/ACM Transactions on Computational Biology and Bioinformatics

 

Food and Nutritional Microbiome

Microbiomes Associated With Foods From Plant and Animal Sources – Karen G. Jarvis – Frontiers in Microbiology

Fecal microbiota responses to bran particles are specific to cereal type and in vitro digestion methods that mimic upper gastrointestinal tract passage – Yunus Emre Tuncil – Journal of Agricultural and Food Chemistry

Gut carbohydrate inhibits GIP secretion via a microbiota/SCFA/FFAR3 pathway – : Eun-Young Lee – Journal of Endocrinology

Review: Human Breast Milk Bacteriome in Health and Disease – Anna Ojo-Okunola – Nutrients

Relative Validity and Reproducibility of a Food Frequency Questionnaire to Assess Nutrients and Food Groups of Relevance to the Gut Microbiota in Young Children – Claudia Leong – Nutrients

 

Other

Surface Exposure and Packing of Lipoproteins into Outer Membrane Vesicles Are Coupled Processes in Bacteroides – Ezequiel Valguarnera – mSphere

The Transferable Resistome of Produce – Khald Blau – mBio

November 7, 2018

There’s lots of new work to catch up on! Some highlights include the skin virome in patients with immune deficiency, a mechanism for host-microbe mutualism in zebrafish, ecological pressures in soil that lead to smaller genomes, and a book chapter about the future of microbial forensics.

General Microbiome
Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness – Wen C. Aw – PLOS Genetics

Antifungal immune responses: emerging host–pathogen interactions and translational implications – Vinod Kumar – Genome Medicine

Pregnancy and early life
Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy. – Liisa Hantsoo – Brain, Behavior, and Immunity

Enabling precision medicine in neonatology, an integrated repository for preterm birth research – Marina Sirota – Scientific Data

Associations of birth mode with cord blood cytokines, white blood cells, and newborn intestinal bifidobacteria – Isabel Cristina Ribas Werlang – PLOS One

HPV infection and bacterial microbiota in breast milk and infant oral mucosa – Heidi Tuominen – PLOS One

Human skin microbiome
Expanded skin virome in DOCK8-deficient patients – Osnat Tirosh – Nature Medicine

Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris – George Zhanel – Antimicrobial Agents and Chemotherapy

Human vaginal microbiome
Preprint: Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota – Kavita Agarwal – bioRxiv

Human multi-site microbiome
The altered human serum metabolome induced by a marathon – Zinandré Stander – Metabolomics

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media
Andrea Coleman
Microbiome

Human gut microbiome
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men – Abigail J. S. Armstrong – Microbiome

Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial – Zhi-Dong Jiang – PLOS One

The long term effect of metabolic profile and microbiota status in early gastric cancer patients after subtotal gastrectomy – Xi-Hsuan Lin – PLOS One

Animal experiments
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish – Annah S Rolig – eLife

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin – Lulu Sun – Nature Medicine

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model – Kazuyuki Kasahara – Nature Microbiology

Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis – Ishfaq Ahmed – PLOS One

Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A. Hatter – PLOS One

Plant, root, and soil microbiome
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W. Sorensen – Nature Microbiology

Decomposition responses to climate depend on microbial community composition -Sydney I. Glassman – PNAS

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities? – J. Parada – Critical Reviews in Biotechnology

Water and extremophile microbiome
Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. – Nyok-Sean Lau – Microbial Ecology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient – Alexandra Meziti – The ISME Journal

Probiotics
Anti-diabetic effects of Lactobacillus casei fermented-yogurt through re-shaping gut microbiota structure in type 2 diabetic rats – Ling Qu – Journal of Agricultural and Food Chemistry

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis – Yanbo Wang – Applied Microbiology and Biotechnology

Techniques
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling – Fei Teng – Scientific Reports

Science career/training and publishing
Preprint: The CURE for Culturing Fastidious Microbes – Arundhati Bakshi – bioRxiv

Meeting Report: Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. – Jacquelyn S. Meisel -Microbiome

In win for open access, two major funders won’t cover publishing in hybrid journals

Microbial Forensics
Book Chapter: Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique – Pankaj Shrivastava – DNA Fingerprinting: Advancements and Future Endeavors

Alyson’s non-microbiology picks
Science candidates prevail in US midterm elections

October 27, 2018

Have a good weekend!

Today, in this Digest we have a good amount of articles, including: a study showing the importance of the gut microbiota in the development of thrombosis; the effect of a probiotic on patients with coronary artery disease; a study about vaginal microbiota and menopause; a study gaining insights about the natural microbiota transmission;  associations between microbiota and exercise, and more!

 

Gut Microbiome

Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential – Sarah M. Skye  – Circulation Research. Comment about this paper in the Editorial: Microbiota-Derived Trimethylamine, The Missing Jigsaw Piece in Thrombosis? – Klytaimnistra Kiouptsi

Gut microbiome and type 2 diabetes: where we are and where to go? – Sapna Sharma – The Journal of Nutritional Biochemistry

The gut microbiome of Mexican children affected by obesity – Otoniel Maya-Lucas – Anaerobe

Endurance exercise and gut microbiota: A review – Núria Mach – Journal of Sport and Health Science

Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice – Zi-Lun Lai – Scientific Reports

Trimethylamine N-Oxide and Risk of Cardiovascular Disease and Mortality – Chanavuth Kanitsoraphan – Current Nutrition Reports

A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area – Timothy P. Jenkins – Scientific Reports

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea – Eric J. Battaglioli – Science Translational Medicine

Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut – Yanan Wang – Gut Microbes

Towards an Individualized Nutrition Treatment: Role of the Gastrointestinal Microbiome in the Interplay Between Diet and Obesity – Solveig A. Adalsteinsdottir – Current Obesity Reports

Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome – Yael R. Nobel – Clinical and Translational Gastroenterology

Clostridial Butyrate Biosynthesis Enzymes Are Significantly Depleted in the Gut Microbiota of Nonobese Diabetic Mice – Alessandro Tanca – mSphere

Modelling the role of microbial p-cresol in colorectal genotoxicity – Eiman Abdulla Al Hinai – Gut Microbes

Diet and Psychosis: A Scoping Review – M. Aucoin – Neuropsychobiology

Minireview: Inflammation and Gut-Brain Axis During Type 2 Diabetes: Focus on the Crosstalk Between Intestinal Immune Cells and Enteric Nervous System – Arnaud Bessac – Frontiers in Neuroscience

Effects of water decontamination methods and bedding material on the gut microbiota – Willie A. Bidot – PLOS One

Timing for the second fecal microbiota transplantation to maintain the long-term benefit from the first treatment for Crohn’s disease – Pan Li – Applied Microbiology and Biotechnology

Gut microbiome disruption altered the biotransformation and liver toxicity of arsenic in mice – Liang Chi – Archives of Toxicology

 

Early Life Microbiome

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort – Maggie A. Stanislawski – mBio

Differences in the fecal microbiota of neonates born at home or in the hospital – Joan L. Combellick – Scientific Reports

Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure – Joann Romano-Keeler – PLOS One

 

Oral, Nasal and Respiratory Tract Microbiome

Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period – Preethi Balan – Frontiers in Microbiology

The Oral Microbiota Is Modified by Systemic Diseases – D.T. Graves – Journal of Dental Research

Prospective Study of Oral Microbiome and Colorectal Cancer Risk in Low-income and African American Populations – Yaohua Yang – International Journal of Cancer

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes – Joshua P. Earl – Microbiome

The effect of maxillary sinus antrostomy size on the sinus microbiome – Alexander S. Kim – International Forum of Allergy & Rhinology

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw Soe Htun – Data in Brief

Variations of the lung microbiome and immune response in mechanically ventilated surgical patients – Ryan M. Huebinger – PLOS One

Root Microbiota in Primary and Secondary Apical Periodontitis – Serge Bouillaguet – Frontiers in Microbiology

 

Reproductive / Urinary Tract Microbiome and Health

Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy – Rebecca M. Brotman – Menopause

Association of Pelvic Inflammatory Disease with Risk of Endometriosis: A Nationwide Cohort Study Involving 141,460 Individuals – Fei-Wu Tai – Journal of Clinical Medicine

 

Beneficial Microbes and Compounds

Lactobacillus plantarum 299v Supplementation Improves Vascular Endothelial Function and Reduces Inflammatory Biomarkers in Men With Stable Coronary Artery Disease – Mobin Malik – Circulation Research. About this article: The Microbiome and Endothelial Function – Jhansi L. Leslie 

Probiotics for gastrointestinal and liver diseases: an updated review of the published literature – Francis E. Dailey – Endocrine, Metabolic & Immune Disorders – Drug Targets

Review: Immunological Tolerance and Function: Associations Between Intestinal Bacteria, Probiotics, Prebiotics, and Phages – Luis Vitetta – Frontiers in Immunology

Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model – Qiaomai Xu – Frontiers in Microbiology

Mixture of Two Lactobacillus plantarum Strains Modulates the Gut Microbiota Structure and Regulatory T Cell Response in Diet-Induced Obese Mice – Jieun Lee – Molecular Nutrition & Food Research

Microbiota stability in healthy individuals after single-dose lactulose challenge-A randomized controlled study – Sandra Y. Wotzka – PLOS One

Review: Interactions of Surface Exopolysaccharides From Bifidobacterium and Lactobacillus Within the Intestinal Environment – Nuria Castro-Bravo – Frontiers in Microbiology

Rapid differentiation of Lactobacillus species via metabolic profiling – Kundi Yang – Journal of Microbiological Methods

Combining probiotics and an angiotensin-II type 1 receptor blocker has beneficial effects on hepatic fibrogenesis in a rat model of nonalcoholic steatohepatitis – Yasuhiko Sawada – Hepatology Research

Antidepressant Effects of Rosemary Extracts Associate With Anti-inflammatory Effect and Rebalance of Gut Microbiota – Ying Guo – Frontiers in Pharmacology

Association of dietary fibre intake and gut microbiota in adults – Daniel Lin – British Journal of Nutrition

Effect of prebiotic and probiotic supplementation on neurodevelopment in preterm very low birth weight infants: findings from a meta-analysis – Ravi Prakash Upadhyay – Pediatric Research

Potential of Maintaining a Healthy Vaginal Environment by Two Lactobacillus Strains Isolated from Cocoa Fermentation – Ana Clara Correia Melgaço – BioMed Research International

Viability of microencapsulated Akkermansia muciniphila and Lactobacillus plantarum during freeze-drying, storage and in vitro simulated upper gastrointestinal tract passage – Martín Sebastián Marcial-Coba – Food & Function

Single probiotic supplement suppresses colitis-associated colorectal tumourigenesis by modulating inflammatory development and microbial homeostasis – Jingjing Rong – Journal of Gastroenterology and Hepatology

Exploring Effects of Chitosan Oligosaccharides on Mice Gut Microbiota in in vitro Fermentation and Animal Model – Chen Zhang – Frontiers in Microbiology

Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique – Akiko Ogawa – Antibiotics

Formation of silver nanoparticles by human gut microbiota – Naiyi Yin – Science of The Total Environment

 

Skin Microbiome

Effect of an Emollient on the Mycobiome of Atopic Dermatitis Patients – Jyotsna Chandra – Journal of Drugs in Dermatology

 

General Microbiome

Transmission modes of the mammalian gut microbiota – Andrew H. Moeller – Science

Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites – Janko Tackmann – Microbiome

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing – Morgane Mailhe – BMC Microbiology

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data – W. Shi – Nucleic Acid Research

Antibiotics and autoimmune and allergy diseases: Causative factor or treatment? – Anna Strzępa – International Immunopharmacology

Pearls: Bacteriophages shift the focus of the mammalian microbiota – Breck A. Duerkop – PLOS Pathogens

 

Environmental Microbiome

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia – Martina Prazeres – Frontiers in Microbiology

17 October,​ 2018

General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

October 14, 2018

General microbiome

16S rRNA Gene Analysis with QIIME2 – Michael Hall, Microbiome Analysis

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt – Gavin M. Douglas, Microbiome Analysis

Single-Cell Genomics of Microbial Dark Matter – Christian Rinke, Microbiome Analysis

An ecosystem framework for understanding and treating disease – Michael E. Hochberg, Foundation for Evolution, Medicine, and Public Health

Diet, Gut Microbes and Host Mate Choice – Philip T. Leftwich, BioEssays

Pregnancy and early life

Methods and Strategies to Examine the Human Breastmilk Microbiome – Lauren LeMay-Nedjelski, Microbiome Analysis

Multi-site human microbiome

Potential mechanisms linking gut microbiota and portal hypertension – Gyorgy Baffy, Liver International

Enlisting commensal microbes to resist antibiotic-resistant pathogens –  James W. Keith, Journal of Experimental Medicine

Human oral microbiome

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials – Christopher Rahimi, Biomicrofluidics

The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms – E. L. Sweeney, Scientific Reports

Human skin microbiome

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes – David L. A. Wood, mBio

Human gut microbiome

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien, Gut Pathogens

Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers – Takuji Gotoda, Helicobacter

Animal microbiome

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere – Alejandra Hernandez-Agreda, mBio

Host differentiation and compartmentalization of microbial communities in the azooxanthelate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean – Aschwin H. Engelen, Frontiers in Microbiology

Comparison of intestinal microbes in female and male Chinese concave‐eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities – Yilin Shu, Microbiology Open

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis – Chenhe Wang, Microbiology Open

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging – Marie Lisandra Zepeda Mendoza, Acta Veterinaria Scandinavica

Animal experiments 

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury – Saisai Cheng, mSystems

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows – Gareth Frank Difford, Plos Genetics

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice – Takao Nagano, Food Chemistry

Lichen microbiome

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota – Tomislav Cernava, ISME

Plant, root, and soil microbiome

Short-term effect of Eucalyptusplantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange – Caroline A. Cuer, Scientific Reports

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea – Jong-Shik Kim, Plos One

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil – Diana Navrátilová, FEMS Microbiology Ecology

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas – Maarten Van Geel, FEMS Microbiology Ecology

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes – Praveen Satapute, Science of The Total Environment

Soil Nutrient Status and Microbial Communities as Influenced by Bio-Fuel Trees Plantation – Agnes Imoya P. O., Environment and Ecology

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam – Tong Jia, Current Microbiology

Effects of wine-cap Strophariacultivation on soil nutrients and bacterial communities in forestlands of northern China – Sai Gong, PeerJ

Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed – Ozgul Calicioglu, Biotechnology for Biofuels

Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture – Oscar M. Rollano-Peñaloza, Cogent Biology

Water, wastewater, and extremophile microbiome

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system – Stefan Thiele, Microbiology Open

The effects of litter quality and living plants on the home-field advantage of aquatic macrophyte decomposition in a eutrophic urban lake, China – Van Biak Luai, Science of The Total Environment

The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health – Gary Klase, Science of The Total Environment

Changes in the drinking water microbiome: effects of water treatments along the flow of two drinking water treatment plants in a urbanized area, Milan (Italy) – Antonia Bruno, Frontiers in Microbiology

Organic particles: heterogeneous hubs for microbial interactions in aquatic ecosystems – Mina Bizic-Ionescu, Frontiers in Microbiology

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands – Yan Zhang, Environmental Pollution

A nearly uniform distributional pattern of heterotrophic bacteria in the Mariana Trench interior – Jiwei Tian, Deep Sea Research Part I: Oceanographic Research Papers

Patterns of permissiveness towards broad host range plasmids in microbial communities across the urban water cycle in Europe – Arnaud Dechesne, Abstract from 17th International Symposium on Microbial Ecology

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP – Ana C. Reis, Applied Microbiology and Biotechnology

Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi – Giulia Spini, Frontiers in Microbiology

Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences – Chase P. Donnelly, HCNSO Student Theses and Dissertations

Antarctic heterotrophic bacterium Hymenobacter nivis P3Tdisplays light‐enhanced growth and expresses putative photoactive proteins – Mia Terashima, Environmental Microbiology Reports

Microbial genomics

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing – Robert Dyrdak, bioRxiv

Leveraging single-cell genomics to expand the fungal tree of life – Steven R. Ahrendt, Nature Microbiology

Microbes in space

Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere – Patricia Fajardo-Cavazos, Scientific Reports

Food microbiology

Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India – Surajit De Mandal, AMB Express

Probiotics / prebiotics

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Rodrigo Carvalho, Scientific Reports

In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota – Sophie Fehlbaum, International Journal of Molecular Sciences

Techniques

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics – Charlotte Mappa, Environmental Science and Pollution Research

 

October 10, 2018

Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens