November 13, 2018

Today’s Digest features several soil and environmental microbiome papers, including the effect of fire on soil ecosystems, insights into the freshwater microbiome associated with the world’s largest mining disaster, applications of soils in forensics, and chemical leaching from LCD screens due to synergistic bacteria. Plus, check out some animal work in marine invertebrates (Sea stars and Ascidians) as well as minks, flying squirrels, and bees!

Pregnancy and early life
The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn – Xuanyi Meng -Journal of Crohn’s and Colitis

Human multi-site microbiome
Shared gut, but distinct oral microbiota composition in primary Sjögren’s syndrome and systemic lupus erythematosus – Taco A. van der Meulen – Journal of Autoimmunity

Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children – Mona Samra – International Archives of Allergy and Immunology

Review: Repertoire of bacterial species cultured from the human oral cavity and respiratory tract – Maxime DM Fonkou – Future Microbiology

Gut-brain axis
Schizophrenia and gut-flora related epigenetic factors – Chuanjun Zhuo – Progress in Neuro-Psychopharmacology and Biological Psychiatry

The structure of resilience in irritable bowel syndrome and its improvement through hypnotherapy: Cross-sectional and prospective longitudinal data – Johannes Peter – PLOS One

Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety – Hajara Aslam – Nutritional Neuroscience

Chronic alcohol exposure induced gut microbiota dysbiosis and its correlations with neuropsychic behaviors and brain BDNF/Gabra1 changes in mice – Zheng Xu – Biofactors

Microbial treatment: the potential application for Parkinson’s disease – Xin Fang – Neurological Sciences

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. – Egle Cekanaviciute – mSystems

Human gut microbiome
The effect of drinking water pH on the human gut microbiota and glucose regulation: results of a randomized controlled cross-over intervention – Tue H. Hansen – Scientific Reports

Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7–18 years old children from the American Gut Project – Jinbing Bai – Pediatric Obesity

Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. – Bastiaan W Haak – Journal of Antimicrobial Chemotherapy

Helicobacter pylori Infection: New Facts in Clinical Management. – Peter Malfertheiner – Current Treatment Options in Gastroenterology

Animal experiments
The protective effects of fecal microbiota transplantation in an experimental model of necrotizing enterocolitis – Christian Prado – Journal of Pediatric Surgery

Intestinal Snakeskin Limits Microbial Dysbiosis during Aging and Promotes Longevity – Anna M. Salazar – iScience

Animal microbiome
Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling – Melanie M. Lloyd – Scientific Reports

Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host–Symbiont Dynamics Plasticity Affect Invasion Capacity?– Hila Dror – Microbial Ecology

Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons – Nicole R. Compo – PLOS One

Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem – Po-Yu Liu – Microbial Ecology

Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers – Shao K. Huang – mSystems

Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish – Kristian Daly – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome
Fire modulates ecosystem functioning through the phylogenetic structure of soil bacterial communities – Eduardo Pérez-Valera – Soil Biology and Biochemistry

Assessment of soil microbial communities involved in cellulose utilization at two contrasting Alpine forest sites – José A. Siles – Soil Biology and Biochemistry

Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach – Fen-Guo Zhang – Microbial Ecology

Influence of different biological control agents and compost on total and nitrification driven microbial communities at rhizosphere and soil level in a lettuce – Fusarium oxysporum f. sp. lactucae pathosystem – Maria Alexandra Cucu – Journal of Applied Microbiology

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. – Fan Wang – AMB Express

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands. – Mónica A. Vásquez Piñeros – Applied Microbiology and Biotechnology

Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield – Jay Prakash Singh – Ecotoxicology and Environmental Safety

Applying microbial biogeography in soil forensics – Habteab Habtom – Forensic Science International: Genetics

eDNA metabarcoding supporting community assessment of environmental stressor in a field-based sediment microcosm study – Jianghua Yang – Environmental Science and Technology

Water and extremophile microbiome
Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods – Mohamed Amine Gomri – Annals of Microbiology

Anaerobic biological treatment of industrial saline wastewater: Fixed bed Reactor performance and analysis of the microbial community structure and abundance – Mariem Jeddi – Environmental Technology

Microbiome triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems – Karin Hellauer – Environmental Science and Technology

Insights on the freshwater microbiomes metabolic changes associated with the world’s largest mining disaster – Marcelle C. Cordeiro – Science of the Total Environment

Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge – Sean Ting-Shyang Wei – mSystems

Built environment
Leaching of indium from end-of-life LCD panels via catalysis by synergistic microbial communities – Yaling Xie – Science of the Total Environment

Probiotics/Prebiotics
Probiotic and synbiotic therapy in the critically ill: State of the art – James M. Davison – Nutrition

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers. – Leen Boesmans – mSystems

Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions – Yunus E. Tuncil – Scientific Reports

Bioinformatics
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks – Demetrius DiMucci – mSystems

Techniques
A tridecaptin-based fluorescent probe for differential staining of Gram-negative bacteria. – Wei Wang – Analytical and Bioanalytical Chemistry

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity – Jeremiah J. Minich – mSystems

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

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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

October 23, 2018

Here comes today’s Microbiome Digest featuring the recent articles on microbial methane oxidizers, sulfidic waters, PM exposure effect on airway microbiome, dysbiotic state of spring fever, diets targeting microbiome and be a cure, peri-implantitis, effect of age and inflammation on mice microbiome, diet effect on monkeys microbiome, fecal microbial transplant in UC patients, cervical microbiome, functional repertoire of ETEC and Bifidobacterium, bile duct inflammation causing microbes, role of probiotics. HAPPY READING.

EVENTS, JOBS, SCHOLARSHIPS:

Commonwealth PhD Scholarships – Study at UK University

ENVIRONMENTAL MICROBIOME:

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers – He Z – Environ Pollut

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters – Deja-Sikora E – Microb Ecol

HUMAN RESPIRATORY MICROBIOME:

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure – Wang L – Ecotoxicol Environ Saf

ORAL MICROBIOME:

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children – Chen B – Int Immunopharmacol

The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis – Kröger A – J Clin Periodontol

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis – Boyer E – Sci Rep

Effects of antimicrobial peptide GH12 on the cariogenic properties and composition of a cariogenic multispecies biofilm – Jiang W – Appl Environ Microbiol
GUT MICROBIOME:

Review: Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota – Liu L – Int J Biol Macromol

Polysaccharides from Laminaria japonica alleviated metabolic syndrome in BALB/c mice by normalizing the gut microbiota – Duan M – Int J Biol Macromol.

Gut microbiota translocation promotes autoimmune cholangitis – Ma HD – J Autoimmun

Competitive lottery-based assembly of selected clades in the human gut microbiome – Verster AJ- Microbiome

Mini-Review : Leaky Gut, Leaky Brain? – Obrenovich MEM – Microorganisms

REPRODUCTIVE MICROBIOME:

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study – Arokiyaraj S –
Sci Rep

ANIMAL MODEL MICROBIOME:

Long-term intake of Lactobacillus paracasei KW3110 prevents age-related chronic inflammation and retinal cell loss in physiologically aged mice – Morita Y – Aging

Targeted Diet Modification Reduces Multiple Sclerosis-like Disease in Adult Marmoset Monkeys from an Outbred Colony – Kap YS – J Immuno

FUNCTIONAL REPERTOIRE INSIGHTS:

Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells – Verma R – Sci Immunol.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933 – Feuerbaum S – Int J Med Microbiol.

PLANT MICROBIOME:

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales – Li HY- Microbiome

METHODS:

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study – Jitsumura M – BMJ Open

PROBIOTICS:

Probiotics in Autoimmune and Inflammatory Disorders – Liu Y – Nutrients

NON-MICROBIOME PICK:

Preprint: Segregational drift and the interplay between plasmid copy number and evolvability – Judith Ilhan- Biorxiv

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 11, 2018

The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

September 28, 2018

Happy Friday! Today we have a long Digest with several interesting reviews and preprints. Learn about the fallopian tube microbiome, the bacterial communities in Icelandic volcanic deposits, the effect of ammonia on anaerobic digesters, skin defense peptides that modulate a frog’s resistance to a pathogen, and a new tool for constructing pan-genomes from shotgun metagenomic data. Enjoy!

General Microbiome
The mammalian mycobiome: A complex system in a dynamic relationship with the host
– Ghee Chuan Lai – WIREs Systems Biology and Medicine

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. – Shao-peng Li – ISMEJ

Pregnancy and Early Life
Fallopian tube microbiota: evidence beyond DNA. -Elise S Pelter – Future Microbiology

Human Oral Microbiome
Titanium as a modifier of the peri‐implant microbiome structure – Diane Daubert – Clinical Implant Dentistry and Related Research

Human Gut Microbiome
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. – Yan He – Microbiome

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease – Federica Ungaro – Gut Microbes

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. – Ravinder Nagpal – Journal of Diabetes Research

Preprint: Social relationships, social isolation, and the human gut microbiota – Kimberly Dill-McFarland – bioRxiv

Review: Gut Microbiota: IgA Protects the Pioneers – Whitman B. Schofield – Current Biology

Review: The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders. – Heather K. Hughes – Current Neurology and Neuroscience Reports

Animal Experiments
Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. – Valentino Le Noci – Cell Reports

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells – A. Butera – Scientific Reports

Fermented Astragalus in diet altered the composition of fecal microbiota in broiler chickens – Hongxing Qiao – AMB Express

Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan‐rich hemicellulose extract in diet – Yvonne Konkol – BJU International

Animal Microbiome
Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. – Sandra V. Flechas – ISMEJ

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. – Xingyong Chen – PLoS One

Plant, root, and soil microbiome
Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals. – Si-jia Liu – Science of The Total Environment

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.– Bo Byloos – BMC Microbiology

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. – Samiran Banerjee – Ecology and Evolution

Water and Extremophile Microbiome
Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities – António Louvado – Environmental Science and Pollution Research

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre – J. C. Robidart – ISMEJ

Food and Industrial Microbiology
Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study – Elsa Sandberg Nielsen – Food & Function

Relationship between microbial community, operational factors and ammonia inhibition resilience in anaerobic digesters at low and moderate ammonia background concentrations. – Y. Lu – New Biotechnology

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae. – Seungdae Oh – Microbial Ecology

Bioinformatics
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. – Florian Plaza Oñate – Bioinformatics

Preprint: A unified framework for unconstrained and constrained ordination of microbiome read count data – Stijn Hawinkel – bioRxiv