Author Archives: JP Cardenas

November 26, 2019

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Have a nice day! Today in this Digest, we have papers about the microbiome and colorectal carcinoma and autism spectrum disorder, as well as studies about skin microbiota. We have also a set of papers about the effect of diet or probiotics in different animal systems, as well as some studies in insects. 

 

Human and General Microbiome

Resistant starch: impact on the gut microbiome and health – Peter DeMartino – Current Opinion in Biotechnology

Mucosal cancer-associated microbes and anastomotic leakage after resection of colorectal carcinoma – Kosuke Mima – Surgical Oncology

Mycobacterial immunomodulation and viral manipulation of neuronal copper efflux in the setting of sporadic Parkinson’s disease: A multi – hit, outside – in hypothesis of its pathogenesis – George D.Vavougios – Medical Hypotheses

Specificity of gut microbiota in children with autism spectrum disorder in Slovakia and its correlation with astrocytes activity marker and specific behavioural patterns – A.Tomova – Physiology & Behavior

Small intestinal bacterial overgrowth is associated with Diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance – Kang-Qi Wu – Scandinavian Journal of Gastroenterology 

Probiotics of Diverse Origin and Their Therapeutic Applications: A Review – Monika Yadav – Journal of the American College of Nutrition 

Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease – Shivani Kansal – Journal of Pediatric Gastroenterology and Nutrition

Dataset of the microbiome composition in skin lesions caused by lumpy skin disease virus via 16s rRNA massive parallel sequencing – Sören Hansen – Data in Brief 

Characterization of Skin Microbiome in Tinea Pedis – Xiaoping Liu – Indian Journal of Microbiology

Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants – Lahari Das –  Indian Journal of Microbiology

Vertical selection for nuclear and mitochondrial genomes shapes gut microbiota and modifies risks for complex diseases – Youjie Zhang – Physiological Genomics

The relationship of gastric microbiota and Helicobacter pylori infection in pediatrics population – Ruixue Miao – Helicobacter

The impact of vitamin B12 deficiency on infant gut microbiota – Perran Boran – European Journal of Pediatrics

Novel Therapies for Treatment of Food Allergy – Sultan Albuhairi – Immunology and Allergy Clinics

Structural and Functional Bases of Genitourinary Syndrome of Menopause – A. K. Pichigina – Bulletin of Experimental Biology and Medicine

The role of bacteria and its derived metabolites in chronic pain and depression: Recent findings and research progress – Shan Li – International Journal of Neuropsychopharmacology

Microbial supernatants from Mobiluncus mulieris, a bacteria strongly associated with spontaneous preterm birth, disrupts the cervical epithelial barrier through inflammatory and miRNA mediated mechanisms – Carolynn M. Dude – Anaerobe

Overview of prospects for inflammation pathways in autism spectrum disorders – H.Turbé – L’Encéphale

 

Animal Microbiome and Animal Experiments

The effect of nitrite and sulfide on the antioxidant capacity and microbial composition of the intestines of red swamp crayfish, Procambarus clarkii – Kun Guo – Fish & Shellfish Immunology

Feed supplementation with inulin on broiler performance and meat quality challenged with Clostridium perfringens: Infection and prebiotic impacts – Andréia Guaragni – Microbial Pathogenesis

Strain specific stress-modulating effects of candidate probiotics: a systematic screening in a mouse model of chronic restraint stress – Lotta K. Stenman – Behavioural Brain Research

Effects of the solubility of yeast cell wall preparations on their potential prebiotic properties in dogs – Stephanie de Souza Theodoro – PLoS One

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster – Gabrielle M. Solomon – PeerJ

Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies – Rittik Deb​ – PeerJ

Kestose supplementation exerts bifidogenic effect within fecal microbiota and increases fecal butyrate concentration in dogs – Kaori Ide – Journal of Veterinary Medical Science

Interactions between host and gut microbiota in domestic pigs: a review – Yadnyavalkya Patil – Gut Microbes

Absorptive transport of amino acids by the rat colon – Yuxin Chen – Gastrointestinal and Liver Physiology

Video: Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization – Jessica N. Witchley – JoVE

Video: Infecting Mice with Malassezia spp. to Study the Fungus-Host Interaction – Florian Sparber – JoVE

 

Plant and Soil Microbiome

Assisted phytoremediation of chromium spiked soils by Sesbania Sesban in association with Bacillus xiamenensis PM14: A biochemical analysis – Bashir Ud Din – Plant Physiology and Biochemistry

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds – Sanderson Tarciso Pereira de Sousa – Ecotoxicology and Environmental Safety

November 19, 2019

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Have a nice Tuesday! Today, in this Digest we have several papers about the microbiome and respiratory health.  We have also papers about the detection of archaeal species in caries biofilm, microbiome and cancer, and microbiome changes by the use of fish oil and their effect on (TMAO)-exacerbated atherogenesis. And of course, more papers… 

 

Human and General Microbiome

Minireview: The Microbiome, Malignant Fungating Wounds, and Palliative Care – Mridula Vardhan – Frontiers in Cellular and Infection Microbiology

Gut microbiota: from the forgotten organ to a potential key player in the pathology of Alzheimer disease – Dong-oh Seo – The Journals of Gerontology

Presence of Archaea in dental caries biofilms – Naile Dame-Teixeira – Archives of Oral Biology

Increased Moraxella and Streptococcus following severe bronchiolitis is associated with recurrent wheezing – Jonathan M. Mansbach  – Journal of Allergy and Clinical Immunology

Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction – Xiaojin Dong – Investigative Ophthalmology & Visual Science 

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – Plos One

Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome – Salahuddin Khan – Frontiers in Cellular and Infection Microbiology

Review: Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD) – Hannah E. O’Farrell – Journal of Thoracic Disease 

Review: COPD and the gut-lung axis: the therapeutic potential of fibre – Annalicia Vaughan – Journal of Thoracic Disease 

Review: Chronic obstructive pulmonary disease (COPD) and lung cancer: common pathways for pathogenesis – Brielle A. Parris – Journal of Thoracic Disease 

The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis – Francesco De Seta – Frontiers in Microbiology

Gut Microbiota in Bipolar Depression and Its Relationship to Brain Function: An Advanced Exploration – Qiaoqiao Lu – Frontiers in Psychiatry

Fish oil is more potent than flaxseed oil in modulating gut microbiota and reducing trimethylamine-N-oxide (TMAO)-exacerbated atherogenesis – Zouyan He – Journal of Agricultural and Food Chemistry 

Characterization of gut microbiota in children with pulmonary tuberculosis – Weiran Li – BMC Pediatrics

Editorial: Bugs, Drugs, and Shrugs – James T. Rosenbaum – Arthritis and Rheumatology

Opinion: Harnessing the Microbiome for Pancreatic Cancer Immunotherapy – Gerardo A. Vitiello – Trends in Cancer

 

Animal Microbiome / Animal Experiments

Review: Maternal imprinting of the neonatal microbiota colonization in intrauterine growth restricted piglets: a review – Lili Jiang – Journal of Animal Science and Biotechnology

Colonization of the gut microbiota of honey bee (Apis mellifera) workers at different developmental stages – Xiang Dong – Microbiological Research 

Effects of oral exposure to titanium dioxide nanoparticles on gut microbiota and gut-associated metabolism in vivo – Zhangjian Chen – Nanoscale

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish – M. Carla Piazzon – Frontiers in Microbiology

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection – Liming Gu – Frontiers in Microbiology

Fuzhuan brick tea attenuates high-fat diet-induced obesity and associated metabolic disorders by shaping gut microbiota – Dongmin Liu – Journal of Agricultural and Food Chemistry 

 

Plant Microbiome

Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification – Bruna Alicia Rafael de Paiva – Plant Disease

Beneficial Plant Microorganisms Affect the Endophytic Bacterial Communities of Durum Wheat Roots as Detected by Different Molecular Approaches – Monica Agnolucci –  Frontiers in Microbiology

 

Methods

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations – Doratha A. Byrd – Plos One

 

Bioinformatics

Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities – Laura M Zingaretti – Bioinformatics

 

Other papers

Antibiotic exposure and risk of Parkinson’s disease in finland: A nationwide case-control study – Tuomas H. Mertsalmi – Movement Disorders

 

November 12, 2019

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Have a nice day! Today we have reviews about the “hologenome” concept, the influence of stress on IBD flares in children and adults and microbiome and liver disease. In addition, we have articles about the effect of UV light on skin microbiota, alligator microbiome, and more!

 

Human and General Microbiome

Perspective: The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis – Adena Collens – Molecular and Developmental Evolution

Review: Stress Triggers Flare of Inflammatory Bowel Disease in Children and Adults – Yue Sun – Frontiers in Pediatrics

Review: Current US Food and Drug Administration-Approved Pharmacologic Therapies for the Treatment of Irritable Bowel Syndrome with Diarrhea – Darren M. Brenner – Advances in Therapy

Review: Microbiome Modulation in Liver Disease – Eamonn M.M. Quigley – Clinical Liver Disease

Viewpoint: How the joint study of the microbiota and metabolites in different body fluids may aid in the identification of novel disease mechanisms – Jordi Mayneris‐Perxachs – The FEBS Journal

Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis – Nupur K. Das – Cell Metabolism

Characteristics of Gut Microbiota in Patients With Rheumatoid Arthritis in Shanghai, China – Yang Sun – Frontiers in Cellular and Infection Microbiology

Using compositional principal component analysis to describe children’s gut microbiota in relation to diet and body composition – Claudia Leong – The American Journal of Clinical Nutrition

Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome – Else S. Bosman – Frontiers in Microbiology

The Therapeutic Effect of 1,8-Cineol on Pathogenic Bacteria Species Present in Chronic Rhinosinusitis – Matthias Schürmann – Frontiers in Microbiology

Potential correlation between dietary fiber suppresses microbial conversion of choline to trimethylamine and formation of methylglyoxal – Qian Li – Journal of Agricultural and Food Chemistry

 

Animal Microbiome

Host-associated microbiomes drive structure and function of marine ecosystems – Laetitia G. E. Wilkins – PLoS Biology

Intake of Watermelon or Its Byproducts Alters Glucose Metabolism, the Microbiome, and Hepatic Proinflammatory Metabolites in High-Fat-Fed Male C57BL/6 J Mice – Alexandra R Becraft – The Journal of Nutrition

Mixed mode bacterial transmission in the common brooding coral Pocillopora acuta – Katarina Damjanovic – Environmental Microbiology

The Effect of Milk Replacer Composition on the Intestinal Microbiota of Pre-ruminant Dairy Calves – James Badman – Frontiers in Veterinary Sciences

Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator – Ke-Yi Tang – Frontiers in Microbiology

A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein – Fan Zhao – Frontiers in Microbiology

Microbiota assessment across different developmental stages of Dermacentor silvarum (Acari: Ixodidae) revealed stage-specific signatures – Zhang Ruiling – Ticks and Tick-borne Diseases

 

Food Microbiome

Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry – Pedro Rodríguez-López – International Journal of Food Microbiology

 

Environmental Microbiome

Response mechanism of microbial community to the environmental stress caused by the different mercury concentration in soils – Lei Wang – Ecotoxicology and Environmental Safety

 

Other papers

The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions – Eoghan M. Smyth – Frontiers in Microbiology 

 

Methods and Techniques

Review: A Bioinformatics Guide to Plant Microbiome Analysis – Rares Lucaciu – Frontiers in Plant Sciences

Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin – Paul Metz – Frontiers in Cellular and Infection Microbiology

Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study – Jinbing Bai – JMIR Medical Informatics

Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia – So Nakagawa – Clinical and Translational Immunology 

November 5, 2019

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Today, in this brief digest:  microbiome and metabolic signatures in IBS, the influence of US immigration on antimicrobial resistance gene spreading, the importance of microbiota delivery, the potential role of the microbiome in head and neck cancer oncogenesis, and more other papers. Have a nice day!

 

Human or General Microbiome

The internationalization of human microbiome research – Ana Maria Porras – Current Opinion in Microbiology 

Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome – Shengtao Zhu – Frontiers in Cellular and Infection Microbiology 

Incidence of Bloodstream Infections, Length of Hospital Stay, and Survival in Patients With Recurrent Clostridioides difficile Infection Treated With Fecal Microbiota Transplantation or Antibiotics: A Prospective Cohort Study – Gianluca Ianiro – Annals of Internal Medicine

Delivery to the gut microbiota: A rapidly proliferating research field – Adi Seifert – Advances in Colloid and Interface Science

Potential role of microbiome in oncogenesis, outcome prediction and therapeutic targeting for head and neck cancer – Ester Orlandi – Oral Oncology

Alterations in Oral Microbiota in HIV are Related to Decreased Pulmonary Function – Libing Yang – American Journal of Respiratory and Critical Care Medicine

Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life – Marta Reyman – Nature Communication

Periodontopathogenic microbiota, infectious mechanisms and preterm birth: analysis with structural equations (cohort-BRISA) – Elisa Miranda Costa – Archives of Gynecology and Obstetrics

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut – Quentin Le Bastard – Clinical Infectious Diseases

 

Beneficial compounds and microbes

Changes in stool frequency following chicory inulin consumption, and effects on stool consistency, quality of life and composition of gut microbiota – Anthony W. Watson – Food Hydrocolloids

Prophages in Lactobacillus reuteri are associated with fitness trade-offs but can increase competitiveness in the gut ecosystem – Jee-Hwan Oh – Applied and Environmental Microbiology

 

Animal Microbiome / Animal Experiments

Effect of Metformin on Short-Term High-Fat Diet-Induced Weight Gain and Anxiety-Like Behavior and the Gut Microbiota – Shuqin Ji – Frontiers in Endocrinology 

Both gut microbiota and cytokines act to atherosclerosis in ApoE-/- mice – Qiuxia Liu – Microbial Pathogenesis 

The Effect of Clostridium butyricum on Gut Microbiota, Immune Response and Intestinal Barrier Function During the Development of Necrotic Enteritis in Chickens – Ting Huang – Frontiers in Microbiology

Lactic Acid Treatment of Cereals and Dietary Phytase Modified Fecal Microbiome Composition Without Affecting Expression of Virulence Factor Genes in Growing Pigs – Jutamat Klinsoda – Frontiers in Microbiology

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus) – Corey C. Holt – The ISME Journal 

An antibiotic depleted microbiome drives severe Campylobacter jejuni-mediated Type 1/17 colitis, Type 2 autoimmunity and neurologic sequelae in a mouse model – Phillip T. Brooks – Journal of Neuroimmunology

 

Environmental Microbiome

Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study – Xiaole Yin – Environment International

 

Bioinformatics

Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data – Nidhi Shah – Frontiers in Genetics

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families – Yan Wang – Genome Biology

 

Techniques

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing – Shailesh K. Shahi – JoVE

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study – Gabriela Guimaraes Sousa Leite – BMC Microbiology

September 26, 2019

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Have a nice day! Today, in this digest we have a good number of papers, including those associated with beneficial microbes, compounds, and interventions. Some highlights: host-microbiome evolution, microbiome and urinary tract infections, the first reported bloodstream infection caused by gut-habiting Prevotella species, microbiome activity in halitosis, and more! Enjoy.   

 

General or Human Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – PNAS

Review: Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome – Catherine S. Forster – Topics in Spinal Cord Injury Rehabilitation 

Review: A critical review on diet-induced microbiota changes and cardiovascular diseases – Muthukumaran Jayachandran – Critical Reviews in Food Science and Nutrition 

Review: Microbiota: a novel regulator of pain – Manon Defaye – Journal of Neural Transmission

Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults – Wei Ye – Journal of Breath Research

An Infectious Diseases Perspective on Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children – Jillian M Cotter – Journal of the Pediatric Infectious Diseases Society

First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report – Patrizia Posteraro – Gut Pathogens

Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential – Ran Guo – British Journal of Anaesthesia

The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis – Martinna Bertolini – Journal of Fungi

Microbiome Influence in the Pathogenesis of Prion and Alzheimer’s Diseases – Valeria D’Argenio – International Journal of Molecular Sciences

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO) – Sarah M. Mitchell – Nutrients

Potential Strategies in the Prevention of Nonsteroidal Anti-inflammatory Drugs-Associated Adverse Effects in the Lower Gastrointestinal Tract – Chuan-Guo Guo – Gut and Liver

 

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe – Trym T Flygel – The Journal of Infectious Diseases

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment – Nai-Lun Yeh – Clinical Drug Investigation

The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants – Masaru Tanaka – Gut Microbes

 

Animal Microbiome

Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice – Lucia Hrncirova – Microorganisms

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model –  Matthew F. Warren – Nutrients

Microbiota, Gut Health and Chicken Productivity: What Is the Connection? – Juan M. Diaz Carrasco – Microorganisms

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets – Raphaële Gresse – Microorganisms 

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring – Pedro Soares-Castro – Scientific Reports

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish – Fotini Kokou – Nature Microbiology

Beneficial Microbes and Compounds

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly – Kerry L. Ivey – mBio

Oral Administration of β-Glucan and Lactobacillus plantarum Alleviates Atopic Dermatitis-like Symptoms – In Sung Kim – Journal of Microbiology and Biotechnology

Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract – Sara Dizzell – Cells (MPDI)

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress – Te-Hsuan Tung – Biomolecules

The Potential Impact of Probiotics on the Gut Microbiome of Athletes – Laura Wosinska – Nutrients

Royal Jelly and Its Components Promote Healthy Aging and Longevity: From Animal Models to Humans – Hiroshi Kunugi – International Journal of Molecular Sciences

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond – Carrie A. M. Wegh – International Journal of Molecular Sciences

Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates – Camilla Itapary dos Santos – Pathogens

Metabolic and Vascular Effect of the Mediterranean Diet – Antonino Tuttolomondo – International Journal of Molecular Sciences

 

Environmental Microbiome

Unveiling resistome profiles in the sediments of an Antarctic volcanic island – V.B. Centurion – Environmental Pollution

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea – Nojood A. Aalismail – Scientific Reports

 

Bioinformatics

The EFI Web Resource for Genomic Enzymology Web Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways – Rémi Zallot – Biochemistry

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification – Florian P Breitwieser – Biochemistry

 

Methods

Review: Common principles and best practices for engineering microbiomes – Christopher E. Lawson – Nature Reviews Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome – Oskar Hickl – Microorganisms

Optimizing bacterial DNA extraction in urine – Matthew M. Munch – PLoS One

 

September 20, 2019

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Have a nice day! In this digest, an interesting study about the relationship between peripheral serotonin synthesis and host glucose homeostasis, as well as another study showing the long-term maintained high levels of Proteobacteria in Crohn’s disease. And, of course, more papers!

 

Human and General Microbiome

Are we Ready for a “Microbiome-Guided Behaviour” Approach? – Andrea Lavazza – Cambridge Quarterly of Healthcare Ethics

The gut microbiome regulates host glucose homeostasis via peripheral serotonin – Alyce M. Martin – PNAS

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis – M. K. Vester-Andersen – Scientific Reports

The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge – Roma Bhuta – JNCI Monographs

Time to test antibacterial therapy in Alzheimer’s disease – Francesco Panza – Brain

Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities – Qiang Zeng – Scientific Reports

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples – Sonia Tarallo – mSystems

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador – María Fernanda Zurita – Gut Microbes 

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – BJOG

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results – Lihong Chen – Digestive Diseases and Sciences

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome – Carrie E. Jung – Scientific Reports

Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood – N. Markova – Scientific Reports

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review – Maria Manuela Estevinho – Clinical Gastroenterology and Hepatology

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients – Anuradha Ravi – Microbial Genomics

Complex interactions between the microbiome and cancer immune therapy – Drew J. Schwartz – Critical Reviews in Clinical Laboratory Sciences

Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite – Bruno Faivre – International Journal for Parasitology

Small talk: microbial metabolites involved in the signaling from microbiota to brain – Giorgia Caspani – Current Opinion in Pharmacology

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients – Solveig Tangedal – PLoS One

 

Animal Microbiome / Animal Experiments

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster – Seth M. Rudman – PNAS

Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress – Kai Zhang – Translational Psychiatry

Adenovirus infection is associated with altered gut microbial communities in a non-human primate – Wasimuddin – Scientific Reports

 

Beneficial Microbes and Compounds

Honey Polyphenols Ameliorate DSS-induced Ulcerative Colitis Via Modulating Gut Microbiota in Rats – Haoan Zhao – Molecular Nutrition and Food Research

ω-3 PUFAs Alleviate High-fat Diet Induced Circadian Intestinal Microbes Dysbiosis – Lifeng Gui – Molecular Nutrition and Food Research

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34 – Wimonrat Panpetch – Gut Microbes

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects –  Baltasar Mayo – Nutrients

Dietary cranberry suppressed colonic inflammation and alleviated gut microbiota dysbiosis in dextran sodium sulfate-treated mice – Xiaokun Cai – Food and Function

 

Food Microbiome

Deciphering the microbiome shift during fermentation of medicinal plants – Martina Köberl – Scientific Reports

 

Plant Microbiome

The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces – Jennifer W. Edmonds – Antonie van Leeuwenhoek

 

Extremophiles

A shared core microbiome in soda lakes separated by large distances – Jackie K. Zorz – Nature Communications

 

Methods

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method – Sukithar K. Rajan – PLoS One

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing – Emma E. Ilett – Scientific Reports

 

August 15, 2019

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Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

August 13, 2019

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Have a good Tuesday!  Today we have a brief digest, covering papers about Staphylococcus and Skin infections and the gut microbiome and Insomnia disorder, in addition with different studies in mice and a report showing genetic relationships between plants and bacterial community configuration. 

 

Human or General Microbiome

Review: Protective effect of the “food-microorganism-SCFAs” axis on colorectal cancer: from basic research to practical application – Han Shuwen – Journal of Cancer Research and Clinical Oncology

Strains of Staphylococcus aureus that Colonize and Infect Skin Harbor Mutations in Metabolic Genes – Karen P. Acker – IScience

Inflamm-aging micrornas may integrate signals from food and gut microbiota by modulating common signalling pathways – Laura Teodori – Mechanisms of Ageing and Development

Gut Microbiota as a Subjective Measurement for Auxiliary Diagnosis of Insomnia Disorder – Bingdong Liu – Frontiers in Microbiology

 

Animal Microbiome

Adhesive Bifidobacterium Induced Changes in Cecal Microbiome Alleviated Constipation in Mice – Linlin Wang – Frontiers in Microbiology

Short-term dietary restriction in old mice rejuvenates the aging-induced structural imbalance of gut microbiota – Ting Zeng – Biogerontology

Species-specific effects of arsenic on the soil collembolan gut microbiota – Yi-Fei Wang – Ecotoxicology and Environmental Safety

Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill – Ruiqun Chen – Journal of Ethnopharmacology

Age- and diet-specific effects of chronic exposure to chlorpyrifos on hormones, inflammation and gut microbiota in rats – Jin-Wang Li – Pesticide Biochemistry and Physiology

High-throughput 16S rRNA gene sequencing reveals that 6-hydroxydopamine affects gut microbial environment – Jin Gyu Choi – PLoS ONE

 

Plant Microbiome

Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization – Rafael Soares Correa de Souza – Frontiers in Microbiology

 

Non-Microbiology Picks

Science–graphic art partnerships to increase research impact – Colin K. Khoury – Communications Biology

August 3, 2019

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Have a happy weekend! Today, in this Digest: an interesting study of the human placenta microbiome, papers showing associations between microbiome and pancreatic or lung cancer, and an update of the pathogenesis of bacterial vaginosis. In addition, a paper showing that the microbiome in primates has a different evolutionary pattern in comparison with the host.  Enjoy!

 

Human and General Microbiome

Human placenta has no microbiome but can contain potential pathogens – Marcus C. de Goffau – Nature

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer – Roberto Mendez – Carcinogenesis

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints – Andres Gomez – mSphere

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules – Yijiu Ren – Translational Lung Cancer Research

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis – Christina A Muzny – The Journal of Infectious Diseases

Review: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health – Aimeé Parker – Gut Microbes

Editorial: The only thing that stops a bad microbiome, is a good microbiome – Jessica R. Galloway-Peña – Haematologica

Review: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation – Andrew J. McBain – Clinical Microbiology Reviews

News: Microbiome therapeutics go small molecule – Megan Cully – Nature Reviews Drug Discovery

Pharmacomicrobiomics informs clinical pharmacogenomics – Theodora Katsila – Future Medicine

Each Additional Day of Antibiotics is Associated with Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients – Ashley M Rooney, BSc – Clinical Infectious Diseases

Prevention and treatment of recurrent Clostridioides difficile infection – Jae Shin – Current Opinion in Infectious Diseases

An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia – Wenkui Dai – Gigascience

Review: Connection between gut microbiome and the development of obesity – Cuiting Zhi – European Journal of Clinical Microbiology & Infectious Diseases

Animal Microbiome

Hyperuricemia is associated with impaired intestinal permeability in mice – Daxing Xu – Gastrointestinal and Liver Physiology

 

Beneficial compounds and Foods

Prevention of Vascular Inflammation by Pterostilbene via Trimethylamine-N-Oxide Reduction and Mechanism of Microbiota Regulation – Yen‐Chun Koh – Molecular Nutrition and Food Research

Interactions of tea polyphenols with intestinal microbiota and their implication for cellular signal conditioning mechanism – Yongyong Li – Journal of Food Biochemistry

Hass Avocado Inclusion in a Weight-Loss Diet Supported Weight Loss and Altered Gut Microbiota: A 12-Week Randomized, Parallel-Controlled Trial – Susanne M Henning – Current Developments in Nutrition

 

Plant Microbiome

Host plant-dependent effects of microbes and phytochemistry on the insect immune response – Su’ad A. Yoon – Oecologia

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria – Barney A. Geddes – Nature Communications 

July 27, 2019

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Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology